Alignments for a candidate for acs in Pseudomonas litoralis 2SM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Pseudomonas litoralis 2SM5

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_090271513.1 BLU11_RS00320 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_900105005.1:WP_090271513.1
          Length = 647

 Score =  860 bits (2221), Expect = 0.0
 Identities = 405/646 (62%), Positives = 500/646 (77%), Gaps = 5/646 (0%)

Query: 1   MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQG-KILDWIKPYQKVKNTS 59
           M +I +H +         ++   YE +Y+QSI  PDTFW EQ  + +DW++P+ K+  ++
Sbjct: 1   MYEIEQHKVSEAARRDTHLDADGYERLYRQSIEQPDTFWAEQATRFVDWMQPWSKIHESN 60

Query: 60  FAPGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCR 119
              G  +  W+ DG LN++ANC+DRHL +  D+TAIIWEGDD S+ +HISY+ELH+ VCR
Sbjct: 61  MDKGEAA--WFIDGKLNVSANCIDRHLAKRADQTAIIWEGDDPSEDRHISYRELHQQVCR 118

Query: 120 FANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSN 179
            AN L   G+KKGD V +YMPM+PEAA AMLAC RIGAVHSV+FGGFSP+A+  RI ++ 
Sbjct: 119 LANVLKARGVKKGDRVCLYMPMIPEAAFAMLACTRIGAVHSVVFGGFSPDALRDRIQNAE 178

Query: 180 SRLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHD 239
            R+VIT+DEGVR G+SIPLK+NVD AL +     V  VV +KRTG  I W E RD+W H+
Sbjct: 179 CRVVITADEGVRGGKSIPLKQNVDKALAD--CPDVHTVVTVKRTGADIPWHEHRDVWCHE 236

Query: 240 LVEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGD 299
                SD  + E M++EDPLFILYTSGSTGKPKGVLHTTGGYL+  ALT  YVFDYH G+
Sbjct: 237 ACAAVSDVCEPEPMDSEDPLFILYTSGSTGKPKGVLHTTGGYLLSTALTHHYVFDYHEGE 296

Query: 300 IYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPT 359
           +YWCTADVGWVTGHSY++YGPL  GATTLMFEGVP +P  +R   +VDKH+VNI YTAPT
Sbjct: 297 VYWCTADVGWVTGHSYIVYGPLCNGATTLMFEGVPTYPNASRCWDIVDKHKVNIFYTAPT 356

Query: 360 AIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETG 419
           AIRALMA GD+ ++ T R+SLR+LGSVGEPINPEAWEWY+  +G+ +CPVVDTWWQTETG
Sbjct: 357 AIRALMALGDEPVKSTSRASLRLLGSVGEPINPEAWEWYYHVVGDSRCPVVDTWWQTETG 416

Query: 420 GFMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFG 479
             +I PLPGAT+LK GSATRPFFGV+PAL DN+GN L G  +G+LVI  SWP Q RT++G
Sbjct: 417 SILIAPLPGATDLKPGSATRPFFGVEPALYDNDGNELHGVADGNLVIKRSWPSQIRTVYG 476

Query: 480 DHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAH 539
           D++RF  TYFST+K +YF+GDGARRDEDGYYWITGRVDDVLN+SGHR+GTAE+ESALV H
Sbjct: 477 DNQRFIDTYFSTYKGVYFTGDGARRDEDGYYWITGRVDDVLNISGHRIGTAEVESALVLH 536

Query: 540 PKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWT 599
             +AEAAVVG PH+IKGQAIYAYV   H   PS EL A+++ +V +++G  A PD + W 
Sbjct: 537 DAVAEAAVVGCPHDIKGQAIYAYVMPMHNATPSDELLADLKVYVSEQVGAFAKPDFIQWA 596

Query: 600 DSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
             LPKTRSGKIMRRILRKIA  +   LGDTSTL+DP VV++L+E +
Sbjct: 597 PGLPKTRSGKIMRRILRKIACDELDTLGDTSTLSDPTVVDELIEHR 642


Lambda     K      H
   0.317    0.135    0.421 

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: 1413
Number of extensions: 56
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: 652
Length of database: 647
Length adjustment: 38
Effective length of query: 614
Effective length of database: 609
Effective search space:   373926
Effective search space used:   373926
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_090271513.1 BLU11_RS00320 (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.3721802.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 1036.7   0.0          0 1036.5   0.0    1.0  1  NCBI__GCF_900105005.1:WP_090271513.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900105005.1:WP_090271513.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1036.5   0.0         0         0       4     628 ..      21     640 ..      18     641 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1036.5 bits;  conditional E-value: 0
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkva 75 
                                           ++ y++ly+++ie+p++fwa++a++ ++w++p++k+ ++++++ +++Wf dg+lnvs+nc+drh++kr+d++a
  NCBI__GCF_900105005.1:WP_090271513.1  21 ADGYERLYRQSIEQPDTFWAEQATRFVDWMQPWSKIHESNMDKgEAAWFIDGKLNVSANCIDRHLAKRADQTA 93 
                                           678*************************************9999***************************** PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           iiwegd+++e  r+++Y+el+++vcrlanvlk+ Gvkkgdrv++Y+pmipea++amlac+RiGavhsvvf+Gf
  NCBI__GCF_900105005.1:WP_090271513.1  94 IIWEGDDPSE-DRHISYRELHQQVCRLANVLKARGVKKGDRVCLYMPMIPEAAFAMLACTRIGAVHSVVFGGF 165
                                           ********96.9************************************************************* PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221
                                           s++al++Ri++ae+++vitadeg+Rggk+i+lk++vd+al++++ +v++v+ vkrtg+++  w+e rDvw +e
  NCBI__GCF_900105005.1:WP_090271513.1 166 SPDALRDRIQNAECRVVITADEGVRGGKSIPLKQNVDKALADCP-DVHTVVTVKRTGADIP-WHEHRDVWCHE 236
                                           *******************************************9.6*************66.*********** PP

                             TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvt 294
                                           +++  +s+ cepe++dsedplfiLYtsGstGkPkGvlhttgGyll +alt++yvfd+++++++wCtaDvGWvt
  NCBI__GCF_900105005.1:WP_090271513.1 237 ACAA-VSDVCEPEPMDSEDPLFILYTSGSTGKPKGVLHTTGGYLLSTALTHHYVFDYHEGEVYWCTADVGWVT 308
                                           ***5.******************************************************************** PP

                             TIGR02188 295 GhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlg 367
                                           GhsYivygPL+nGattl+fegvptyp+asr+w++++k+kv+ifYtaPtaiRalm+lg+e vk++++ slr+lg
  NCBI__GCF_900105005.1:WP_090271513.1 309 GHSYIVYGPLCNGATTLMFEGVPTYPNASRCWDIVDKHKVNIFYTAPTAIRALMALGDEPVKSTSRASLRLLG 381
                                           ************************************************************************* PP

                             TIGR02188 368 svGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkev 440
                                           svGepinpeaweWyy+vvG+++cp+vdtwWqtetG+ili+plpg at+lkpgsat+P+fG+e+++ d++g+e+
  NCBI__GCF_900105005.1:WP_090271513.1 382 SVGEPINPEAWEWYYHVVGDSRCPVVDTWWQTETGSILIAPLPG-ATDLKPGSATRPFFGVEPALYDNDGNEL 453
                                           ********************************************.6*************************** PP

                             TIGR02188 441 eeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlg 513
                                           +  ++ g Lvik++wPs++rt+ygd++rf++tYf+++kg+yftGDgarrd+dGy+wi+GRvDdv+n+sGhr+g
  NCBI__GCF_900105005.1:WP_090271513.1 454 HGVAD-GNLVIKRSWPSQIRTVYGDNQRFIDTYFSTYKGVYFTGDGARRDEDGYYWITGRVDDVLNISGHRIG 525
                                           98777.89***************************************************************** PP

                             TIGR02188 514 taeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvve 586
                                           tae+esalv h+avaeaavvg p++ikg+ai+a+v+ ++++++++e l ++lk  v++++g++akpd i++++
  NCBI__GCF_900105005.1:WP_090271513.1 526 TAEVESALVLHDAVAEAAVVGCPHDIKGQAIYAYVMPMHNATPSDE-LLADLKVYVSEQVGAFAKPDFIQWAP 597
                                           *********************************************5.************************** PP

                             TIGR02188 587 elPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                            lPktRsGkimRR+lrkia +e ++lgd+stl+dp+vv+el+e
  NCBI__GCF_900105005.1:WP_090271513.1 598 GLPKTRSGKIMRRILRKIACDElDTLGDTSTLSDPTVVDELIE 640
                                           ****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (647 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: 00:00:00.02
# Mc/sec: 19.32
//
[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