Alignments for a candidate for acs in Azospirillum thiophilum BV-S

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Azospirillum thiophilum BV-S

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_045580972.1 AL072_RS06780 acetate--CoA ligase

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



>NCBI__GCF_001305595.1:WP_045580972.1
          Length = 646

 Score =  932 bits (2408), Expect = 0.0
 Identities = 439/643 (68%), Positives = 515/643 (80%), Gaps = 3/643 (0%)

Query: 1   MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           M+  S +PV+PE+AA    +   Y  MY+QSV +P+ FW E  KR+DWIKP++ VK   F
Sbjct: 1   MTDNSFFPVKPEIAATAHVNAEAYARMYEQSVNDPEAFWGEHGKRIDWIKPYSKVKDVDF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF 120
           +   V I+WF DGTLNVS NC+DRHLA RGDQ AI++EGDDP  S+ ITY+ELHE+V + 
Sbjct: 61  NGD-VHIRWFHDGTLNVSANCIDRHLATRGDQTAILFEGDDPGVSKAITYKELHEKVSRL 119

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           AN L+   V +GD VTIY+PMIPEA  AMLACTRIGAIHS+VFGGFSP++L  RI+DC S
Sbjct: 120 ANVLKKNGVRKGDRVTIYLPMIPEAAYAMLACTRIGAIHSIVFGGFSPDSLKDRIVDCDS 179

Query: 181 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL 240
             VIT+DEGLR G+K+ LKAN D A+       ++ V+V K TGGN+ W + RD+WY + 
Sbjct: 180 HFVITSDEGLRGGRKVPLKANADKAVAG--APMVRHVLVVKHTGGNVAWTEGRDLWYHEE 237

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300
           M+     C P+EM AE+ LFILYTSGSTGKPKGV HTTGGYL+YA++THE VFDY+ GE+
Sbjct: 238 MESVSADCPPEEMSAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHEYVFDYKQGEV 297

Query: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA 360
           YWCTADVGWVTGH+YIVYGPLANGATTL+FEGVP YPD++R  ++IDKHKVNI YTAPTA
Sbjct: 298 YWCTADVGWVTGHSYIVYGPLANGATTLMFEGVPTYPDVSRFWQVIDKHKVNIFYTAPTA 357

Query: 361 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA 420
           IR++M +G   V+    +SLR+LGSVGEPINPEAW WYY  VG +RCPIVDTWWQTETG 
Sbjct: 358 IRSLMREGEGPVKTTSRASLRVLGSVGEPINPEAWLWYYNVVGDARCPIVDTWWQTETGG 417

Query: 421 TLMSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGD 480
            L++PL GA G KPGSA +PFFGV P +VDN G ++EG  EGNL I D+WPG  RT+YGD
Sbjct: 418 ILITPLIGAIGQKPGSATKPFFGVQPVVVDNEGQVLEGETEGNLCIADAWPGMMRTVYGD 477

Query: 481 HDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           H+RFV TYF TF G YFTGDG RRDADGY+WITGRVDDV+NVSGHRMGTAE+ESA+VAHP
Sbjct: 478 HERFVQTYFSTFAGKYFTGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVAHP 537

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAP 600
           KVAEAAVVG PHD+KGQGIY YVTLN GE P+E LR EL  WVRKEIGPIASPD+IQWAP
Sbjct: 538 KVAEAAVVGYPHDLKGQGIYAYVTLNAGETPTEELRKELVAWVRKEIGPIASPDLIQWAP 597

Query: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLID 643
           GLPKTRSGKIMRRILRKIA  E+D LGD STLADPGVV  LID
Sbjct: 598 GLPKTRSGKIMRRILRKIAANEHDALGDTSTLADPGVVTDLID 640


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: 1474
Number of extensions: 66
Number of successful extensions: 3
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: 646
Length adjustment: 38
Effective length of query: 613
Effective length of database: 608
Effective search space:   372704
Effective search space used:   372704
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_045580972.1 AL072_RS06780 (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.3808695.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 1039.1   0.1          0 1038.9   0.1    1.0  1  NCBI__GCF_001305595.1:WP_045580972.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001305595.1:WP_045580972.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1038.9   0.1         0         0       3     628 ..      20     640 ..      18     641 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1038.9 bits;  conditional E-value: 0
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekrkdk 73 
                                           ++e+y+++ye++++dpe+fw++++k +++w+kp++kv+d +++   +++Wf+dg+lnvs+nc+drh+++r d+
  NCBI__GCF_001305595.1:WP_045580972.1  20 NAEAYARMYEQSVNDPEAFWGEHGK-RIDWIKPYSKVKDVDFNGdvHIRWFHDGTLNVSANCIDRHLATRGDQ 91 
                                           7899*********************.5**************9987899************************* PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +ai +egd++g  s+++tY+el+++v+rlanvlk+ Gv+kgdrv+iYlpmipea++amlac+RiGa+hs+vf+
  NCBI__GCF_001305595.1:WP_045580972.1  92 TAILFEGDDPGV-SKAITYKELHEKVSRLANVLKKNGVRKGDRVTIYLPMIPEAAYAMLACTRIGAIHSIVFG 163
                                           ***********7.************************************************************ PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvww 219
                                           Gfs+++l++Rivd+++++vit+deglRgg++++lk+++d+a++ a+ +v++vlvvk+tg +va w+egrD+w+
  NCBI__GCF_001305595.1:WP_045580972.1 164 GFSPDSLKDRIVDCDSHFVITSDEGLRGGRKVPLKANADKAVAGAP-MVRHVLVVKHTGGNVA-WTEGRDLWY 234
                                           *********************************************9.7*************77.********* PP

                             TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292
                                           +e++e+ +sa+c+pe++++edplfiLYtsGstGkPkGvlhttgGyl++a++t++yvfd+k+++++wCtaDvGW
  NCBI__GCF_001305595.1:WP_045580972.1 235 HEEMES-VSADCPPEEMSAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHEYVFDYKQGEVYWCTADVGW 306
                                           *****6.****************************************************************** PP

                             TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365
                                           vtGhsYivygPLanGattl+fegvptypd srfw+vi+k+kv+ifYtaPtaiR+lm++ge  vk +++ slrv
  NCBI__GCF_001305595.1:WP_045580972.1 307 VTGHSYIVYGPLANGATTLMFEGVPTYPDVSRFWQVIDKHKVNIFYTAPTAIRSLMREGEGPVKTTSRASLRV 379
                                           ************************************************************************* PP

                             TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438
                                           lgsvGepinpeaw Wyy+vvG+ +cpivdtwWqtetGgilitpl g a+ +kpgsat+P+fG++++vvd+eg+
  NCBI__GCF_001305595.1:WP_045580972.1 380 LGSVGEPINPEAWLWYYNVVGDARCPIVDTWWQTETGGILITPLIG-AIGQKPGSATKPFFGVQPVVVDNEGQ 451
                                           **********************************************.6************************* PP

                             TIGR02188 439 eveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhr 511
                                            +e e+e g L+i ++wP+m+rt+ygd+erfv+tYf+++ g yftGDg+rrd+dGy+wi+GRvDdvinvsGhr
  NCBI__GCF_001305595.1:WP_045580972.1 452 VLEGETE-GNLCIADAWPGMMRTVYGDHERFVQTYFSTFAGKYFTGDGCRRDADGYYWITGRVDDVINVSGHR 523
                                           ***8777.79*************************************************************** PP

                             TIGR02188 512 lgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilv 584
                                           +gtae+esalv+h++vaeaavvg+p+++kg+ i+a+v+l++g++++ee l+kel ++vrkeigpia+pd i++
  NCBI__GCF_001305595.1:WP_045580972.1 524 MGTAEVESALVAHPKVAEAAVVGYPHDLKGQGIYAYVTLNAGETPTEE-LRKELVAWVRKEIGPIASPDLIQW 595
                                           *********************************************995.************************ PP

                             TIGR02188 585 veelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           ++ lPktRsGkimRR+lrkia++e ++lgd+stl+dp vv +l++
  NCBI__GCF_001305595.1:WP_045580972.1 596 APGLPKTRSGKIMRRILRKIAANEhDALGDTSTLADPGVVTDLID 640
                                           ************************99**************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (646 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: 25.32
//
[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:

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