Alignments for a candidate for acs in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Rhodobacter viridis JA737

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_110807483.1 C8J30_RS18190 acetate--CoA ligase

Query= reanno::pseudo3_N2E3:AO353_03060
         (651 letters)



>NCBI__GCF_003217355.1:WP_110807483.1
          Length = 636

 Score =  833 bits (2153), Expect = 0.0
 Identities = 412/625 (65%), Positives = 477/625 (76%), Gaps = 5/625 (0%)

Query: 22  ATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVDIKWFADGTLNVSYNC 81
           A Y  MY++S+ NPD FW  + KRLDWI P+T VK T F    V IKWF DG LN S NC
Sbjct: 8   AKYLEMYRESIENPDAFWGREGKRLDWITPYTKVKNTDFTFGKVSIKWFEDGVLNASVNC 67

Query: 82  LDRHLAERGDQIAIIWEGDDPAE-SRNITYRELHEQVCKFANALRGQDVHRGDVVTIYMP 140
           +DRHL +R  Q AII+E DDPA  +++ITY+EL E+V + AN L  Q + RGD V IY+P
Sbjct: 68  IDRHLRDRALQTAIIFEPDDPATPAKHITYKELSEKVNRMANVLLSQGIMRGDRVVIYLP 127

Query: 141 MIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITADEGLRAGKKISLKA 200
           MIPEA  AMLAC RIGAIHS+VF GFSP+ALA RI DC +K+VITAD   R G++  LKA
Sbjct: 128 MIPEAAYAMLACARIGAIHSIVFAGFSPDALANRINDCGAKLVITADTAPRGGRRTPLKA 187

Query: 201 NVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDLMKVAGTVCAPKEMGAEEALF 260
           N D AL +   S   + +V K TG  I W   RD+    LM+     C P+ M AE+ LF
Sbjct: 188 NTDAALLH--CSDKVRCLVVKHTGDQISWVHGRDVDLLYLMEHVSPECPPRPMNAEDPLF 245

Query: 261 ILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEIYWCTADVGWVTGHTYIVYGP 320
           ILYTSGSTGKPKGV HTTGGYL+YAA+TH+  FDY+ G+++WCTADVGWVTGH+YI+YGP
Sbjct: 246 ILYTSGSTGKPKGVVHTTGGYLVYAAMTHQYTFDYKDGDVFWCTADVGWVTGHSYIIYGP 305

Query: 321 LANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTAIRAMMAQGTAAVEGADGSSL 380
           LANGATTL+FEGVP +PD  R   + +KHKVN  YTAPTAIRA+M QGT  VE  D SSL
Sbjct: 306 LANGATTLMFEGVPTWPDAGRFWAVCEKHKVNQFYTAPTAIRALMGQGTEWVEKYDLSSL 365

Query: 381 RLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGATLMSPLPGAHGLKPGSAARP 440
           R+LGSVGEPINPEAW WY K+VG+ +CPIVDT+WQTETG  +++PLPGA   KPGSA  P
Sbjct: 366 RVLGSVGEPINPEAWVWYDKHVGKGKCPIVDTFWQTETGGHMITPLPGATATKPGSATNP 425

Query: 441 FFGVVPALVD--NLGNIIEGVAEGNLVILDSWPGQARTLYGDHDRFVDTYFKTFRGMYFT 498
           FFGV P ++D      I E   EG L I DSWPGQ RT++GDHDRF +TYF  +RG YFT
Sbjct: 426 FFGVKPVVLDPQTAVRIGEVECEGVLCISDSWPGQMRTVWGDHDRFQETYFGQYRGYYFT 485

Query: 499 GDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAAVVGVPHDIKGQG 558
           GDG RRD DGY+WITGRVDDV+NVSGHRMGTAE+ESA+VAHP+VAEAAVVG PHDIKGQG
Sbjct: 486 GDGCRRDKDGYYWITGRVDDVINVSGHRMGTAEVESALVAHPQVAEAAVVGYPHDIKGQG 545

Query: 559 IYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMRRILRKI 618
           IY YVTL  G EPSE LR +L  WVR EIGPIASPD+IQWAPGLPKTRSGKIMRRILRKI
Sbjct: 546 IYAYVTLMNGIEPSEDLRKDLVKWVRTEIGPIASPDLIQWAPGLPKTRSGKIMRRILRKI 605

Query: 619 ATGEYDGLGDISTLADPGVVQHLID 643
           A  +Y  LGDISTLADPGVVQ LID
Sbjct: 606 AENDYGALGDISTLADPGVVQELID 630


Lambda     K      H
   0.319    0.136    0.425 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1438
Number of extensions: 60
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 651
Length of database: 636
Length adjustment: 38
Effective length of query: 613
Effective length of database: 598
Effective search space:   366574
Effective search space used:   366574
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_110807483.1 C8J30_RS18190 (acetate--CoA ligase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02188.hmm
# target sequence database:        /tmp/gapView.3301085.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02188  [M=629]
Accession:   TIGR02188
Description: Ac_CoA_lig_AcsA: acetate--CoA ligase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
          0 1023.5   0.0          0 1023.3   0.0    1.0  1  NCBI__GCF_003217355.1:WP_110807483.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003217355.1:WP_110807483.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1023.3   0.0         0         0       4     628 ..       7     630 ..       4     631 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1023.3 bits;  conditional E-value: 0
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 
                                             +y e+y+e+ie+p++fw++++k +l+w++p++kv++++++    ++kWfedg ln+s+nc+drh+++r+ +
  NCBI__GCF_003217355.1:WP_110807483.1   7 GAKYLEMYRESIENPDAFWGREGK-RLDWITPYTKVKNTDFTFgkvSIKWFEDGVLNASVNCIDRHLRDRALQ 78 
                                           5799********************.5**************9877789************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +aii+e d++ + ++++tY+el ++v+r+anvl ++G+ +gdrv+iYlpmipea++amlacaRiGa+hs+vfa
  NCBI__GCF_003217355.1:WP_110807483.1  79 TAIIFEPDDPATPAKHITYKELSEKVNRMANVLLSQGIMRGDRVVIYLPMIPEAAYAMLACARIGAIHSIVFA 151
                                           ************************************************************************* PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvww 219
                                           Gfs++ala+Ri+d+ aklvitad++ Rgg++++lk+++d+al +++++v+ +lvvk+tg++++ w++grDv +
  NCBI__GCF_003217355.1:WP_110807483.1 152 GFSPDALANRINDCGAKLVITADTAPRGGRRTPLKANTDAALLHCSDKVR-CLVVKHTGDQIS-WVHGRDVDL 222
                                           **********************************************9997.9*********76.********* PP

                             TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292
                                             l+e+ +s ec+p+++++edplfiLYtsGstGkPkGv+httgGyl++aa+t++y+fd+kd+d+fwCtaDvGW
  NCBI__GCF_003217355.1:WP_110807483.1 223 LYLMEH-VSPECPPRPMNAEDPLFILYTSGSTGKPKGVVHTTGGYLVYAAMTHQYTFDYKDGDVFWCTADVGW 294
                                           *****6.****************************************************************** PP

                             TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365
                                           vtGhsYi+ygPLanGattl+fegvpt+pda+rfw+v+ek+kv++fYtaPtaiRalm +g+e+v+k+dlsslrv
  NCBI__GCF_003217355.1:WP_110807483.1 295 VTGHSYIIYGPLANGATTLMFEGVPTWPDAGRFWAVCEKHKVNQFYTAPTAIRALMGQGTEWVEKYDLSSLRV 367
                                           ************************************************************************* PP

                             TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvd.eeg 437
                                           lgsvGepinpeaw Wy ++vGk+kcpivdt+WqtetGg++itplpg at++kpgsat+P+fG++++v+d +++
  NCBI__GCF_003217355.1:WP_110807483.1 368 LGSVGEPINPEAWVWYDKHVGKGKCPIVDTFWQTETGGHMITPLPG-ATATKPGSATNPFFGVKPVVLDpQTA 439
                                           **********************************************.6*********************6666 PP

                             TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                            ++ e e +gvL+i+++wP+++rt++gd++rf+etYf +++g+yftGDg+rrdkdGy+wi+GRvDdvinvsGh
  NCBI__GCF_003217355.1:WP_110807483.1 440 VRIGEVECEGVLCISDSWPGQMRTVWGDHDRFQETYFGQYRGYYFTGDGCRRDKDGYYWITGRVDDVINVSGH 512
                                           667799999**************************************************************** PP

                             TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583
                                           r+gtae+esalv+h++vaeaavvg+p++ikg+ i+a+v+l++g+e++e+ l+k+l k+vr+eigpia+pd i+
  NCBI__GCF_003217355.1:WP_110807483.1 513 RMGTAEVESALVAHPQVAEAAVVGYPHDIKGQGIYAYVTLMNGIEPSED-LRKDLVKWVRTEIGPIASPDLIQ 584
                                           ************************************************5.*********************** PP

                             TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           +++ lPktRsGkimRR+lrkiae++  +lgd+stl+dp vv+el++
  NCBI__GCF_003217355.1:WP_110807483.1 585 WAPGLPKTRSGKIMRRILRKIAENDyGALGDISTLADPGVVQELID 630
                                           *************************99***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (636 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.03s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 8.58
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources