GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas simiae WCS417

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate GFF4246 PS417_21750 acetyl-CoA synthetase

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



>FitnessBrowser__WCS417:GFF4246
          Length = 651

 Score = 1298 bits (3359), Expect = 0.0
 Identities = 626/651 (96%), Positives = 637/651 (97%)

Query: 1   MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF
Sbjct: 1   MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF 120
           DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQ AIIWEGDDP+ESR ITYRELHE+VCKF
Sbjct: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQAAIIWEGDDPSESRTITYRELHEEVCKF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS
Sbjct: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180

Query: 181 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL 240
           KVVITADEG+RAGKKI LKANVDDALTNPETSSIQKVIVCKRT GNIKWNQHRDIWYEDL
Sbjct: 181 KVVITADEGIRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTNGNIKWNQHRDIWYEDL 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300
           MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI
Sbjct: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300

Query: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA 360
           YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKI+DKHKVNILYTAPTA
Sbjct: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIVDKHKVNILYTAPTA 360

Query: 361 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA 420
           IRAMMA GTAA EGADGSSLRLLGSVGEPINPEAW+WYYKNVGQSRCPIVDTWWQTETG 
Sbjct: 361 IRAMMASGTAACEGADGSSLRLLGSVGEPINPEAWDWYYKNVGQSRCPIVDTWWQTETGG 420

Query: 421 TLMSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGD 480
            +MSPLPGAH LKPGSAARPFFGVVPALVDNLGN+IEG AEGNLVILDSWPGQARTL+GD
Sbjct: 421 NMMSPLPGAHALKPGSAARPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLFGD 480

Query: 481 HDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           HDRFVDTYFKTFRGMYFTGDGARRD DGY+WITGRVDDVLNVSGHRMGTAEIESAMVAHP
Sbjct: 481 HDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAP 600
           KVAEAAVVGVPHDIKGQGIYVYVTL  GEEP+EALRLELKNWVRKEIGPIASPDVIQWAP
Sbjct: 541 KVAEAAVVGVPHDIKGQGIYVYVTLKNGEEPNEALRLELKNWVRKEIGPIASPDVIQWAP 600

Query: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLIDTHKTMNVA 651
           GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVV HLI+THKTMNVA
Sbjct: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVAHLIETHKTMNVA 651


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: 1751
Number of extensions: 56
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: 651
Length adjustment: 38
Effective length of query: 613
Effective length of database: 613
Effective search space:   375769
Effective search space used:   375769
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 GFF4246 PS417_21750 (acetyl-CoA synthetase)
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.22669.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 1018.4   0.1          0 1018.2   0.1    1.0  1  lcl|FitnessBrowser__WCS417:GFF4246  PS417_21750 acetyl-CoA synthetas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4246  PS417_21750 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1018.2   0.1         0         0       3     628 ..      20     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1018.2 bits;  conditional E-value: 0
                           TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkv 74 
                                         +  +yk++y++++ +p+ fw+++ak+ l+w+kpf++v+++s+++   ++kWf+dg+lnvsync+drh+++r d++
  lcl|FitnessBrowser__WCS417:GFF4246  20 DEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDhhvDIKWFADGTLNVSYNCLDRHLAERGDQA 93 
                                         5679*********************5.*************99887789*************************** PP

                           TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfs 149
                                         aiiwegd+++e sr++tY+el++evc++an+l+ + v++gd v+iY+pmipeav+amlac+RiGa+hsvvf+Gfs
  lcl|FitnessBrowser__WCS417:GFF4246  94 AIIWEGDDPSE-SRTITYRELHEEVCKFANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFS 167
                                         *********96.*************************************************************** PP

                           TIGR02188 150 aealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelv 223
                                         +eala Ri+d+++k+vitadeg+R gk+i+lk++vd+al++ e+ s++kv+v+krt+ +++ w++ rD+w+e+l+
  lcl|FitnessBrowser__WCS417:GFF4246 168 PEALAGRIIDCKSKVVITADEGIRAGKKIPLKANVDDALTNPETsSIQKVIVCKRTNGNIK-WNQHRDIWYEDLM 241
                                         *****************************************9998**************76.************* PP

                           TIGR02188 224 ekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsY 298
                                         +  a + c+p+++++e+ lfiLYtsGstGkPkGv+httgGyll+aalt++ vfd+++++i+wCtaDvGWvtGh+Y
  lcl|FitnessBrowser__WCS417:GFF4246 242 KV-AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEIYWCTADVGWVTGHTY 315
                                         *5.************************************************************************ PP

                           TIGR02188 299 ivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepi 373
                                         ivygPLanGattllfegvp+ypd  r++++++k+kv+i+YtaPtaiRa+m+ g+++ +  d sslr+lgsvGepi
  lcl|FitnessBrowser__WCS417:GFF4246 316 IVYGPLANGATTLLFEGVPNYPDITRVAKIVDKHKVNILYTAPTAIRAMMASGTAACEGADGSSLRLLGSVGEPI 390
                                         *************************************************************************** PP

                           TIGR02188 374 npeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggv 448
                                         npeaw+Wyy++vG+++cpivdtwWqtetGg +++plpg a +lkpgsa++P+fG+ +++vd+ g+ +e  +e g 
  lcl|FitnessBrowser__WCS417:GFF4246 391 NPEAWDWYYKNVGQSRCPIVDTWWQTETGGNMMSPLPG-AHALKPGSAARPFFGVVPALVDNLGNLIEGAAE-GN 463
                                         **************************************.6****************************8777.79 PP

                           TIGR02188 449 LvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvs 523
                                         Lvi ++wP+++rt++gd++rfv+tYfk+++g+yftGDgarrd+dGy+wi+GRvDdv+nvsGhr+gtaeiesa+v+
  lcl|FitnessBrowser__WCS417:GFF4246 464 LVILDSWPGQARTLFGDHDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVA 538
                                         *************************************************************************** PP

                           TIGR02188 524 heavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimR 598
                                         h++vaeaavvgvp++ikg+ i+++v+lk+g+e++e +l+ elk++vrkeigpia+pd i++++ lPktRsGkimR
  lcl|FitnessBrowser__WCS417:GFF4246 539 HPKVAEAAVVGVPHDIKGQGIYVYVTLKNGEEPNE-ALRLELKNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMR 612
                                         **********************************9.5************************************** PP

                           TIGR02188 599 Rllrkiaege.ellgdvstledpsvveelke 628
                                         R+lrkia+ge + lgd+stl+dp vv++l+e
  lcl|FitnessBrowser__WCS417:GFF4246 613 RILRKIATGEyDGLGDISTLADPGVVAHLIE 643
                                         **********9****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (651 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: 11.00
//
[ok]

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

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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