GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Shewanella halifaxensis HAW-EB4

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_012276800.1 SHAL_RS08815 acetate--CoA ligase

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



>NCBI__GCF_000019185.1:WP_012276800.1
          Length = 650

 Score =  985 bits (2546), Expect = 0.0
 Identities = 462/644 (71%), Positives = 536/644 (83%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MS  SLY V  E+AA+ L ++  YK MYQ+S+VNP+GFWRE   R+DWIKPFT VK+TSF
Sbjct: 1   MSTQSLYKVPSEIAANALVNDEQYKKMYQESIVNPEGFWREHGNRIDWIKPFTKVKKTSF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
           DDH++ IKWF DGTLN S NCLDRHL    D++AIIWEGDD  + R +TY +LH +VCKF
Sbjct: 61  DDHNLFIKWFYDGTLNASANCLDRHLENNADKLAIIWEGDDAKDQRTLTYGQLHTQVCKF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALR Q V RGDVVTIYMPM+PEA VAMLAC RIGAIHSVVFGGFSP+++A R+ID  S
Sbjct: 121 ANALRSQGVRRGDVVTIYMPMVPEAAVAMLACARIGAIHSVVFGGFSPDSIASRVIDGNS 180

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           KVVITADEGVRAG+ IPLKAN+D+AL++P+ + ++KVIV KRT G+I W + RDIW++ L
Sbjct: 181 KVVITADEGVRAGRIIPLKANIDEALSHPDVNCVEKVIVMKRTGGDINWVEGRDIWWDSL 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           M  A   C  +EMGAE+ LF+LYTSGSTG PKGV HTT GY++YAA+THE VFDYK  EV
Sbjct: 241 MDTASEHCIAEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYMVYAAMTHEYVFDYKENEV 300

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTADVGW+TGHSY+VYGPLANGAT L+ EGVPNYP   R+ +++D+HKV+ILYTAPT 
Sbjct: 301 YWCTADVGWITGHSYMVYGPLANGATVLIHEGVPNYPSPARLGEMVDRHKVNILYTAPTL 360

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

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           +LISPLPGAT  KPGSATRPFFGV PALVDN+GN+++GA+EGNLVILDSWPGQ RT++GD
Sbjct: 421 ILISPLPGATDTKPGSATRPFFGVQPALVDNMGNIVDGASEGNLVILDSWPGQMRTVFGD 480

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           HDRFV TYFKTF GMYFTGDGA+RDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+VAH 
Sbjct: 481 HDRFVLTYFKTFRGMYFTGDGAKRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHE 540

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

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIET 644
           GLPKTRSGKIMRR LRKIA  E   LGD STLADP V+  LIET
Sbjct: 601 GLPKTRSGKIMRRFLRKIAANEVSNLGDSSTLADPAVIDTLIET 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: 1457
Number of extensions: 52
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 WP_012276800.1 SHAL_RS08815 (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.3039289.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 1024.1   0.1          0 1023.9   0.1    1.0  1  NCBI__GCF_000019185.1:WP_012276800.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000019185.1:WP_012276800.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1023.9   0.1         0         0       3     628 ..      20     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1023.9 bits;  conditional E-value: 0
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkd 72 
                                           + e+yk++y+e+i +pe fw+++++ +++w+kpf+kv+++s+++   ++kWf dg+ln+s+nc+drh+e+++d
  NCBI__GCF_000019185.1:WP_012276800.1  20 NDEQYKKMYQESIVNPEGFWREHGN-RIDWIKPFTKVKKTSFDDhnlFIKWFYDGTLNASANCLDRHLENNAD 91 
                                           6799*********************.5*************99877789************************* PP

                             TIGR02188  73 kvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvf 145
                                           k+aiiwegd+++ d+r+ltY +l+++vc++an+l+++Gv++gd v+iY+pm+pea++amlacaRiGa+hsvvf
  NCBI__GCF_000019185.1:WP_012276800.1  92 KLAIIWEGDDAK-DQRTLTYGQLHTQVCKFANALRSQGVRRGDVVTIYMPMVPEAAVAMLACARIGAIHSVVF 163
                                           *********998.6*********************************************************** PP

                             TIGR02188 146 aGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDv 217
                                           +Gfs++++a+R++d ++k+vitadeg+R g++i+lk+++deal++ +   vekv+v+krtg +++ w+egrD+
  NCBI__GCF_000019185.1:WP_012276800.1 164 GGFSPDSIASRVIDGNSKVVITADEGVRAGRIIPLKANIDEALSHPDVnCVEKVIVMKRTGGDIN-WVEGRDI 235
                                           *********************************************99889*************66.******* PP

                             TIGR02188 218 wweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDv 290
                                           ww++l+++ as++c +e++++edplf+LYtsGstG+PkGvlhttgGy+++aa+t++yvfd+k+++++wCtaDv
  NCBI__GCF_000019185.1:WP_012276800.1 236 WWDSLMDT-ASEHCIAEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYMVYAAMTHEYVFDYKENEVYWCTADV 307
                                           *******6.**************************************************************** PP

                             TIGR02188 291 GWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlssl 363
                                           GW+tGhsY+vygPLanGat l++egvp+yp+++r+ e+++++kv+i+YtaPt+iRalm++g+e+++  d ssl
  NCBI__GCF_000019185.1:WP_012276800.1 308 GWITGHSYMVYGPLANGATVLIHEGVPNYPSPARLGEMVDRHKVNILYTAPTLIRALMAEGKEQFAGFDGSSL 380
                                           ************************************************************************* PP

                             TIGR02188 364 rvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdee 436
                                           r++gsvGepinpeaw+Wy++v+G+ekcpivdtwWqtetGgili+plpg at++kpgsat+P+fG+++++vd+ 
  NCBI__GCF_000019185.1:WP_012276800.1 381 RIMGSVGEPINPEAWRWYNDVIGHEKCPIVDTWWQTETGGILISPLPG-ATDTKPGSATRPFFGVQPALVDNM 452
                                           ************************************************.6*********************** PP

                             TIGR02188 437 gkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsG 509
                                           g+ v+  +e g Lvi ++wP+++rt++gd++rfv tYfk+++g+yftGDga+rd+dGy+wi+GRvDdvinvsG
  NCBI__GCF_000019185.1:WP_012276800.1 453 GNIVDGASE-GNLVILDSWPGQMRTVFGDHDRFVLTYFKTFRGMYFTGDGAKRDEDGYYWITGRVDDVINVSG 524
                                           *****8777.79************************************************************* PP

                             TIGR02188 510 hrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdki 582
                                           hrlgtae+esalv+he vaeaavvg+p++ikg+ i+a+v+l++g+ e+e el++el+++vrkeig++a+pd i
  NCBI__GCF_000019185.1:WP_012276800.1 525 HRLGTAEVESALVAHEFVAEAAVVGYPHDIKGQGIYAYVTLTKGSVETE-ELRQELRQWVRKEIGALATPDLI 596
                                           *******************************************999888.5********************** PP

                             TIGR02188 583 lvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           +++  lPktRsGkimRR+lrkia++e ++lgd stl+dp+v+++l+e
  NCBI__GCF_000019185.1:WP_012276800.1 597 QWAGGLPKTRSGKIMRRFLRKIAANEvSNLGDSSTLADPAVIDTLIE 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 36.80
//
[ok]

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

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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:

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:

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:

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:

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