COMER results

[OPTIONS]
EVAL = 10.0
NOHITS = 700
NOALNS = 700
SHOW = 1
DSCLEN = 1024
DSCWIDTH = 80
ALNWIDTH = 60
X_UNINF = 1
IDENTITY = 90
SHOWCMD = 0
PCFWEIGHT = 1.5
MINALNFRN = 5
MINALNPOS = 10
SUBMAT = Gonnet
SCOADJ = hdpsco
SUPCLT = 5
ADJWGT = 0.33
cADJWGT = 0.33
CVSWGT = 0.15
SSSWGT = 0.12
SSEMODEL = 2
HCFILTER = 0
HCWINDOW = 12
HCLOWENT = 3.3
HCHIGHENT = 3.4
INVLCFILTER = 0
LCFILTEREACH = 1
LCWINDOW = 8
LCLOWENT = 1.6
LCHIGHENT = 1.6
DISTANCE = 12.96
MAPALN = 1
MINPP = 0.28
DSTSEGM = 6
DSTNPOS = 12
DSTSEP6 = 12
DSTGAPL = 24
DSTFREE = 3
DDMSWGT = 0.2
hhsuite_in_use = 1
hhsuite_opt_niterations = 2
hhsuite_opt_evalue = 0.001
hmmer_in_use = 0
hmmer_opt_niterations = 2
hmmer_opt_evalue = 0.001
comer_db = pdb70_220717,swissprot90_2022_03
cother_db = pdb70_211110
hhsuite_db = UniRef30_2022_02
sequence_db = uniref50_2022_08.fasta

>PF11325.10 (sequence)
EITGKIIAILPEQSGTSKNGEWKKQEFVLETEEQYPKKICFEFFGDKIDLLNIQVGDEVKVSFDIEGREWNGRWFNSIRAWRIE
//
>P0C6J7, Duck hepatitis B virus (MSA in A3M format)
MDINASRALANVYDLPDDFFPKIDDLVRDAKDALEPYWKSDSIKKHVLIATHFVDLIEDFWQTTQGMHEIAESLRAVIPPTTTPVPPGYLIQHEEAEEIPLGDLFKHQEERIVSFQPDYPITARIHAHLKAYAKINEESLDRARRLLWWHYNCLLWGEAQVTNYISRLRTWLSTPEKYRGRDAPTIEAITRPIQVAQGGRKTTTGTRKPRGLEPRRRKVKTTVVYGRRRSKSRERRAPTPQRAGSPLPRSSSSHHRSPSPRK
>UniRef100_A0A193AUV5 (1-216) Core n=1 Tax=Tibetan frog hepatitis B virus TaxID=2169919 RepID=A0A193AUV5_9HEPA   Expect=1.5e-46
MDPIVRFSLQLVENLPDDYFPSNDQFLRHAFDVAHLYWEDADNKTfhvqtsrsiyeMILILRTVPPLL-GF--THRQLREHWEYIRdqenwtNQIPIPPYPlppLPHSFPVSI---RDPPLLTQFQRITDRHRelrgavnVGQPNSYRELWMLSEFNRFLGIMIESQTRfLIKRLWYHINCIAWGEATVHNHVAKVRTWLATPPPYRGQNAPIIEEIVEPQR--------------------------------------------------------------------
>UniRef100_A0A0M3P3L7 (22-178) PreC/core protein n=1 Tax=White sucker hepatitis B virus TaxID=1690672 RepID=A0A0M3P3L7_9HEPA   Expect=1.2e-31
MDPLVKAALEGVKDLPHDFFPLLKDQVQFSKDVIKEYNEHHSQNRHVEVINCSLESYDNL-QL------IYA--KVTISNWTAIANNGDSVQVALDENARTGL--------AYIFQST--------------------IEMSIRRKLWWHTNCLMWGESQTAEYTAKLRSWLMTPTSYRNQYAPTIEALTRTVK--------------------------------------------------------------------
>UniRef100_A0A077YVB8 (116-210) Core protein (Fragment) n=1 Tax=Hepatitis B virus TaxID=10407 RepID=A0A077YVB8_HBV   Expect=2.7e-31
------------------------------------------------------------------------------------------------------------------------------------SYVNTNMGLKIRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILSTLP-----------------------------ETTVV--RRRGRSPRRRTPSPRRRRSQSPRRRRSQSRES----
//
>7M1W NMR structure of the Human T-cell leukemia virus 1 matrix protein (MSA in aligned FASTA format)
MGRIFSRSASPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKK----FLKIALETPVWICPINYSLLASLL-PKGYPGRVNEILHILIQTQAQIPSRPAHHHHHH
>UniRef100_Q86918 Gag polyprotein (Fragment) n=1 Tax=Human T-cell leukemia virus type I TaxID=11908 RepID=Q86918_9DELA
MGQIFSRSASPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKsaqlYSSLSLDSPP--SPPREPLRPS------------------------------------
>UniRef100_P0C210 Gag-Pro polyprotein n=1 Tax=Human T-cell leukemia virus 1 (isolate Melanesia mel5 subtype C) TaxID=402046 RepID=PRO_HTL1L
MGQIFPRSANPIPRPPRGLATHHWLNFLQAAYRLEPGPSSYDFHQLKT----VLKMALETPVWMCPINYSLLASLL-PKGYPGQVNEILQVLIQTQTQI-----------
>UniRef100_A0A193H389 Group specific antigen n=1 Tax=Human T-lymphotropic virus 4 TaxID=318279 RepID=A0A193H389_9DELA
MGQTH--ASSPVPKAPRGLSTHHWLNFLQAAYRLQPGPSEFDFHQLRR----FLKLALQTPVWLNPIDYSLLASLI-PKGYPGRVAEIVNILLRAHP-------------
>UniRef100_A0A346CHN5 Gag-Pro-Pol polyprotein n=1 Tax=Bovine leukemia virus TaxID=11901 RepID=A0A346CHN5_BLV
------MGNSPSYNPPAGISPSDWLNLLQSAQRLNPRPSPSDFTDLKN----YIHWFHKTQ----KKPWTFTSGGP-TSCPPGRFGRVPLVLATLNEVLSN---------
>UniRef100_A0A4Y6I0I2 Gag-Pro-Pol polyprotein n=1 Tax=Simian T-lymphotropic virus 1 TaxID=33747 RepID=A0A4Y6I0I2_9STL1
MGLTFSRAASPIPRPPRGLAAHHWLNFLQAAYRLEPGPSAYDFHQLRR----FLKLALETPVWMCPINYSLLASLL-PKGYPGRVNEILNILIQTQTQVPP---------
>UniRef100_O70641 Gag-Pro-Pol polyprotein n=4 Tax=Simian T-lymphotropic virus 2 TaxID=33748 RepID=O70641_9DELA
MGQTYGLSSSPIPKAPRGLSTHHWLNFLQAAYRLQPGPSDFDFQQLRR----FLKLALKTPIWLNPIDYSLLASLI-PKGYPGRTIEIINVLIKNQTSPTP---------
>UniRef100_P03363 Gag-Pro-Pol polyprotein n=26 Tax=Human T-cell leukemia virus 2 TaxID=11909 RepID=POL_HTLV2
MGQIHGLSPTPIPKAPRGLSTHHWLNFLQAAYRLQPRPSDFDFQQLRR----FLKLALKTPIWLNPIDYSLLASLI-PKGYPGRVVEIINILVKNQVSPSA---------
>UniRef100_Q4U0X6 Gag-Pro-Pol polyprotein n=1 Tax=Human T-cell leukemia virus 3 (strain Pyl43) TaxID=406769 RepID=POL_HTL3P
MGKTYSSPVNPIPKAPKGLAIHHWLNFLQAAYRLQPGPSEFDFHQLRK----FLKLAIKTPVWLNPINYSVLARLI-PKNYPGRVHEIVAILIQETPAREA---------
>UniRef100_Q9WNX0 Gag/pX fusion protein (Fragment) n=1 Tax=Human T-cell leukemia virus type I TaxID=11908 RepID=Q9WNX0_9DELA
------------------MAAHHWLNFLQAAYRLEPGPSSYDFHLR----------------------------------------------------------------
>UniRef100_A0A0E3VNR8 Gag-Pro-Pol polyprotein n=1 Tax=Bovine leukemia virus TaxID=11901 RepID=A0A0E3VNR8_BLV
------MGNSPSYNPPAGISPSDWLNLLQSAQRLNPRPSPSDFTDLKN----YIHWFHKTQK--KPWTFTSGGPTScPPGRFGRVPLVLATLNEVLSNE-----------
//
# STOCKHOLM 1.0
#=GF ID   DUF1904
#=GF AC   PF08921.13
#=GF DE   Domain of unknown function (DUF1904)
#=GF AU   Mistry J;0000-0003-2479-5322
#=GF AU   Sammut SJ;0000-0003-4472-904X
#=GF SE   pdb_1u9d
#=GF GA   24.10 24.10;
#=GF TC   24.80 24.60;
#=GF NC   23.90 23.30;
#=GF BM   hmmbuild HMM.ann SEED.ann
#=GF SM   hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
#=GF TP   Domain
#=GF WK   Domain_of_unknown_function
#=GF CL   CL0082
#=GF DR   INTERPRO; IPR015017;
#=GF DR   SO; 0000417; polypeptide_domain;
#=GF CC   This domain is found in a set of hypothetical bacterial
#=GF CC   proteins.
#=GF SQ   9
#=GS Q8RFG4_FUSNN/1-107  AC Q8RFG4.1
#=GS Q188J0_CLOD6/1-108  AC Q188J0.1
#=GS A4J4K9_DESRM/1-107  AC A4J4K9.1
#=GS Q6MPG9_BDEBA/5-112  AC Q6MPG9.1
#=GS Q6F289_MESFL/1-104  AC Q6F289.1
#=GS Q39YS1_GEOMG/1-102  AC Q39YS1.1
#=GS Q8EEJ0_SHEON/1-109  AC Q8EEJ0.1
#=GS A1S6E5_SHEAM/1-107  AC A1S6E5.1
#=GS Q9KU16_VIBCH/1-106  AC Q9KU16.1
#=GS Q9KU16_VIBCH/1-106  DR PDB; 1U9D B; 1-106;
#=GS Q9KU16_VIBCH/1-106  DR PDB; 1U9D A; 1-106;
Q8RFG4_FUSNN/1-107             MPHLKIRGIEKNLIVENSKEIIDELTKIIGCDRNWFTIEHQNTKYIFDGKIVDGYTFVELYWFARDEKIKKEVADFLTKFIKKI.NNNKDCCIIFFTLTGDNYCDNGE.
Q188J0_CLOD6/1-108             MPQIKIRGINENDICKISEKMINDLVEAVKCPRDYFEIECIKSVAIRDGKIADVYPFVEVAWFDRGQEVQDIVARIITDSIRNN.LDVESMDLAFTVFEKEKYYENGEH
A4J4K9_DESRM/1-107             MPQIIIRGIEPKKIMPISNDLISNLEKIIGCPREDLTLECIPSIFVKDGSIDAGYPFVEIGWFDRGQSVQDLVAKEITNQIQR..AGFESVDIMFTTFTKNKYYENGQH
Q6MPG9_BDEBA/5-112             MPHIRMRAVKKEHVQLLSDSLAKELAPAMKTPVDNFTFELVQTQFFSGGQQTDSYPFIEVLWFARSQEVQDECASIITRQIKSI.ADYEDVVIVFQVLAKEAYYENGIH
Q6F289_MESFL/1-104             MPILKFNGTTEEKVKEYSKK.INEIADLIVSKPEAILMMVNNNNIFVAKNTNKRI.YVEVDWLKRSEESRVLLVQHLTNFFG...NQGVNVSVKFTEINNDLYVNNEKR
Q39YS1_GEOMG/1-102             MPYLRFKGFDEGFLRKLGPLVVEEFSRVAVVPPEVVKIELLNIVQITATPRS.....LEIFIFPRDQKKHDAIAATLAGILGR..YGYDDVHIFFVLLSPSLYYKEGIP
Q8EEJ0_SHEON/1-109             MPHISMRGLPQAVVAELSQTLLQSLAAICKGKAESFTLDWIPSISYRNGRIDQRFVQIELLWFPVDPDIHLKVEQTIRLAVTEAYPELTQIAVMFLSLTPSASYRGGQH
A1S6E5_SHEAM/1-107             MPHLRIRGLASDAVARLSRELPARLAAITATEVSSYTMEWIPSQFFQQGEACQPLVMVEVLWFQRNESTQDDMEACIREHLLA..ETQLSVAVIFIGLDKRGYYRDGRH
Q9KU16_VIBCH/1-106             MPHLRFRAVEAHIVESLVPTLLNELSSLLSTARNAFTFELINTQYFAEGGV...YPMVEVLWFGREQQTQDQIAQVITDQIRQLLGADSHLAVVFIPLQRTAYYLDGQH
#=GR Q9KU16_VIBCH/1-106  SS    --EEEEESS-HHHHHHHHHHHHHHHHHHHT--GGG-EEEE-------TT-B...--EEEEEES---HHHHHHHHHHHHHHHHHHH-TT---EEEEEE--GGG-EETTEE
#=GC SS_cons                   --EEEEESS-HHHHHHHHHHHHHHHHHHHT--GGG-EEEE-------TT-B...--EEEEEES---HHHHHHHHHHHHHHHHHHH-TT---EEEEEE--GGG-EETTEE
#=GC seq_cons                  MPal+hRGlppphltclSpplls-Luplhsssh-saThEhlso.hhpsGphsp.ashVElhWFsRspcspDtlAphITptlpp..sshpslslhFhsLspstYYcsGpH
//

Submitting...
Queued.
Running...
Preparing input...
  The queries in the input have different formats
Searching sequences for MSAs...
  1/4 queries done (time distr.: 100% MSA)
  2/4 queries done (time distr.: 100% MSA)
  3/4 queries done (time distr.: 100% MSA)
  4/4 queries done (time distr.: 100% MSA)
Buiding MSAs by sequence search and constructing profiles...
  1/4 queries done (time distr.: 100% profile construction)
  2/4 queries done (time distr.: 100% profile construction)
  3/4 queries done (time distr.: 100% profile construction)
  4/4 queries done (time distr.: 100% profile construction)
Searching by profile-profile alignment using COMER...
Finalizing results...
Finished.