Alignments for a candidate for acs in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Shewanella loihica PV-4

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate 5209055 Shew_1533 acetyl-CoA synthetase (RefSeq)

Query= reanno::pseudo5_N2C3_1:AO356_18695
         (651 letters)



>FitnessBrowser__PV4:5209055
          Length = 650

 Score =  984 bits (2544), Expect = 0.0
 Identities = 461/644 (71%), Positives = 537/644 (83%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MS  SLY V  E+AA+   ++  YK MYQ+SVVNP+GFWRE  +R+DW+KPFT VK+TSF
Sbjct: 1   MSTQSLYKVPSEIAANAHINDEKYKKMYQESVVNPEGFWREHGQRIDWMKPFTKVKKTSF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
           DDH++ I WF DGTLN S NCLDRHLA+  D++AIIWEGDD ++ R +TY ELH EVCKF
Sbjct: 61  DDHNLSINWFYDGTLNASVNCLDRHLADNADKLAIIWEGDDAADQRTLTYGELHTEVCKF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALR Q V RGDVVT+YMPM+PEA V MLAC RIGAIHSVVFGGFSP+++A R+ID KS
Sbjct: 121 ANALRSQGVRRGDVVTVYMPMVPEAAVVMLACARIGAIHSVVFGGFSPDSIASRVIDGKS 180

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           KVVITADEGVR G+ IPLKAN+D+AL++P+ + ++KVIV +RT   + W + RDI +  L
Sbjct: 181 KVVITADEGVRGGRTIPLKANIDEALSHPDVTCVEKVIVLERTGNPVNWVEGRDIKWASL 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           M+ A   C  +EMGAE+ LF+LYTSGSTG PKGV HTT GYL+YA++THE VFDYK GE+
Sbjct: 241 METASEHCVAEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYLVYASMTHEYVFDYKEGEI 300

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTADVGW+TGHSY+VYGPLANGAT L+ EG+PNYP   R+ ++ID+HKV+ILYTAPT 
Sbjct: 301 YWCTADVGWITGHSYMVYGPLANGATILIHEGIPNYPTPARLGEMIDRHKVNILYTAPTL 360

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IRA+MA G    +G DGSSLR++GSVGEPINPEAW WY++ +G E CPIVDTWWQTETGG
Sbjct: 361 IRALMAEGKEQFDGFDGSSLRIMGSVGEPINPEAWRWYHEVIGHENCPIVDTWWQTETGG 420

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           +LISPLPGAT  KPGSATRPFFGV PALVDN+GN+I+GAAEGNLVILDSWPGQ RT+YGD
Sbjct: 421 ILISPLPGATDTKPGSATRPFFGVQPALVDNMGNIIDGAAEGNLVILDSWPGQMRTVYGD 480

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           HDRF  TYFKTF GMYFTGDGARRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+VAH 
Sbjct: 481 HDRFALTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHE 540

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
            VAEAAVVG PHDIKGQGIY YVTL  G + SE LR EL+ WVRKEIG +A+PD+IQWA 
Sbjct: 541 HVAEAAVVGYPHDIKGQGIYAYVTLTKGTQESEELRQELRQWVRKEIGALATPDLIQWAG 600

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIET 644
           GLPKTRSGKIMRR LRKIA  E   LGD STLADP V+  LIET
Sbjct: 601 GLPKTRSGKIMRRFLRKIAANEVTNLGDASTLADPAVIDTLIET 644


Lambda     K      H
   0.318    0.135    0.418 

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: 1474
Number of extensions: 50
Number of successful extensions: 1
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: 650
Length adjustment: 38
Effective length of query: 613
Effective length of database: 612
Effective search space:   375156
Effective search space used:   375156
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate 5209055 Shew_1533 (acetyl-CoA synthetase (RefSeq))
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.15232.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 1021.6   0.1          0 1021.4   0.1    1.0  1  lcl|FitnessBrowser__PV4:5209055  Shew_1533 acetyl-CoA synthetase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209055  Shew_1533 acetyl-CoA synthetase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1021.4   0.1         0         0       3     628 ..      20     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1021.4 bits;  conditional E-value: 0
                        TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkvaii 77 
                                      + e+yk++y+e++ +pe fw+++++ +++w+kpf+kv+++s+++   +++Wf dg+ln+s+nc+drh+++++dk+aii
  lcl|FitnessBrowser__PV4:5209055  20 NDEKYKKMYQESVVNPEGFWREHGQ-RIDWMKPFTKVKKTSFDDhnlSINWFYDGTLNASVNCLDRHLADNADKLAII 96 
                                      5689********************9.5*************99887789****************************** PP

                        TIGR02188  78 wegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealae 155
                                      wegd++  d+r+ltY el++evc++an+l+++Gv++gd v++Y+pm+pea+++mlacaRiGa+hsvvf+Gfs++++a+
  lcl|FitnessBrowser__PV4:5209055  97 WEGDDAA-DQRTLTYGELHTEVCKFANALRSQGVRRGDVVTVYMPMVPEAAVVMLACARIGAIHSVVFGGFSPDSIAS 173
                                      ****998.6********************************************************************* PP

                        TIGR02188 156 RivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelvekeasaece 232
                                      R++d ++k+vitadeg+Rgg++i+lk+++deal++ +   vekv+v++rtg++v+ w+egrD++w +l+e+ as++c 
  lcl|FitnessBrowser__PV4:5209055 174 RVIDGKSKVVITADEGVRGGRTIPLKANIDEALSHPDVtCVEKVIVLERTGNPVN-WVEGRDIKWASLMET-ASEHCV 249
                                      ***********************************99989*************66.**************6.****** PP

                        TIGR02188 233 pekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGatt 310
                                      +e++++edplf+LYtsGstG+PkGvlhttgGyl++a++t++yvfd+k+++i+wCtaDvGW+tGhsY+vygPLanGat 
  lcl|FitnessBrowser__PV4:5209055 250 AEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYLVYASMTHEYVFDYKEGEIYWCTADVGWITGHSYMVYGPLANGATI 327
                                      ****************************************************************************** PP

                        TIGR02188 311 llfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGke 388
                                      l++eg+p+yp+++r+ e+i+++kv+i+YtaPt+iRalm++g+e+++  d sslr++gsvGepinpeaw+Wy+ev+G+e
  lcl|FitnessBrowser__PV4:5209055 328 LIHEGIPNYPTPARLGEMIDRHKVNILYTAPTLIRALMAEGKEQFDGFDGSSLRIMGSVGEPINPEAWRWYHEVIGHE 405
                                      ****************************************************************************** PP

                        TIGR02188 389 kcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygde 466
                                      +cpivdtwWqtetGgili+plpg at++kpgsat+P+fG+++++vd+ g+ ++  +e g Lvi ++wP+++rt+ygd+
  lcl|FitnessBrowser__PV4:5209055 406 NCPIVDTWWQTETGGILISPLPG-ATDTKPGSATRPFFGVQPALVDNMGNIIDGAAE-GNLVILDSWPGQMRTVYGDH 481
                                      ***********************.6****************************8777.79****************** PP

                        TIGR02188 467 erfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeai 544
                                      +rf  tYfk+++g+yftGDgarrd+dGy+wi+GRvDdvinvsGhrlgtae+esalv+he+vaeaavvg+p++ikg+ i
  lcl|FitnessBrowser__PV4:5209055 482 DRFALTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHEHVAEAAVVGYPHDIKGQGI 559
                                      ****************************************************************************** PP

                        TIGR02188 545 vafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledps 621
                                      +a+v+l++g++e+e el++el+++vrkeig++a+pd i+++  lPktRsGkimRR+lrkia++e ++lgd stl+dp+
  lcl|FitnessBrowser__PV4:5209055 560 YAYVTLTKGTQESE-ELRQELRQWVRKEIGALATPDLIQWAGGLPKTRSGKIMRRFLRKIAANEvTNLGDASTLADPA 636
                                      ***********999.5************************************************************** PP

                        TIGR02188 622 vveelke 628
                                      v+++l+e
  lcl|FitnessBrowser__PV4:5209055 637 VIDTLIE 643
                                      ***9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (650 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 11.86
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 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