Alignments for a candidate for acs in Algoriphagus aquaeductus T4

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Algoriphagus aquaeductus T4

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_111394621.1 CLV31_RS18770 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_003253485.1:WP_111394621.1
          Length = 630

 Score =  728 bits (1878), Expect = 0.0
 Identities = 353/621 (56%), Positives = 445/621 (71%), Gaps = 7/621 (1%)

Query: 28  YQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAANCLDRHLQ 87
           YQ+S+  P+ FW        W K + KV   +F      +KW++  TLN+  N  ++ L 
Sbjct: 15  YQKSVAQPEEFWARIADSFHWRKRWNKVLKWNFE--GPEVKWFDGATLNITENIFEKQLY 72

Query: 88  ENGDRTAIIWEGDDASQ-SKHISYKELHRDVCRFANTLLELGIKKGDVVAIYMPMVPEAA 146
             G+R AIIWE ++  + ++ ++Y++L R+VCRFAN L   GI KGD V IYMPMVPEAA
Sbjct: 73  TIGERPAIIWEPNEPDEPARTLTYRQLFREVCRFANALKAKGIGKGDRVIIYMPMVPEAA 132

Query: 147 VAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPLKKNVDDAL 206
           +AMLACARIGA+HSV+F GFS  ++A RI D  ++ V+TSD   R  + I +K  VD+AL
Sbjct: 133 IAMLACARIGAIHSVVFAGFSSSSLADRINDCQAKAVLTSDGNFRGNKKITVKGVVDEAL 192

Query: 207 KNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAEDPLFILYTSG 266
           +    +SVE V+V KRTG +     GRD WW +++E  SD++ AEEM +ED LFILYTSG
Sbjct: 193 EK---SSVETVIVYKRTGQETTMVPGRDFWWDEVLEGQSDENIAEEMESEDMLFILYTSG 249

Query: 267 STGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGPLACGAT 326
           STGKPKGV+HTTGGY+VY   +F+ VF Y PGD+YWCTADVGW+TGHSY++YGPL  GAT
Sbjct: 250 STGKPKGVVHTTGGYMVYTKYSFENVFQYSPGDVYWCTADVGWITGHSYIVYGPLLAGAT 309

Query: 327 TLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSLRILGSV 386
           TLMFEGVP +P P+R  QV++KHQVN+ YTAPTAIRAL A G + IEG D SSL++LGSV
Sbjct: 310 TLMFEGVPTYPNPSRFWQVIEKHQVNVFYTAPTAIRALQAFGTEPIEGYDLSSLKVLGSV 369

Query: 387 GEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSATRPFFGVQP 446
           GEPIN EAW WY   IG   CP+VDTWWQTETGG +++PL G T  K   AT P  G+Q 
Sbjct: 370 GEPINEEAWHWYHTHIGKGHCPIVDTWWQTETGGILVSPLAGITPTKPAYATLPLPGIQL 429

Query: 447 ALVDNEGNPLEG-ATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFSGDGARRD 505
            +VD EGN L G + EG+L I   WP   RT +GDHER +QTYFST+KNMYF+GDG +RD
Sbjct: 430 CIVDAEGNELTGNSVEGNLCIKFPWPSMIRTTYGDHERCKQTYFSTYKNMYFTGDGVKRD 489

Query: 506 EDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQAIYAYVTL 565
            DGYY I GRVDDV+NVSGHR+GTAE+E+A+  HPK+ E+AVVG PH +KGQ IYAYV  
Sbjct: 490 HDGYYRILGRVDDVINVSGHRMGTAEVENAINEHPKVIESAVVGYPHEVKGQGIYAYVIC 549

Query: 566 NHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKIAAGDTSN 625
           +        L  E++  V K IGP+A PD +     LPKTRSGKIMRRILRK+A G T +
Sbjct: 550 DMTNRTEENLINEIKEMVSKIIGPIAKPDKIQIVPGLPKTRSGKIMRRILRKVAEGSTDS 609

Query: 626 LGDTSTLADPGVVEKLLEEKQ 646
           +GDTSTL DP VVEK++E ++
Sbjct: 610 MGDTSTLLDPEVVEKIIEGRK 630


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: 1311
Number of extensions: 57
Number of successful extensions: 5
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: 630
Length adjustment: 38
Effective length of query: 614
Effective length of database: 592
Effective search space:   363488
Effective search space used:   363488
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_111394621.1 CLV31_RS18770 (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.1436374.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-292  957.8   0.4   1.3e-292  957.6   0.4    1.0  1  NCBI__GCF_003253485.1:WP_111394621.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003253485.1:WP_111394621.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  957.6   0.4  1.3e-292  1.3e-292       5     628 ..       9     627 ..       5     628 .. 0.98

  Alignments for each domain:
  == domain 1  score: 957.6 bits;  conditional E-value: 1.3e-292
                             TIGR02188   5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkvai 76 
                                           + y   y++++++pe+fwa+ a  +++w k ++kvl++++e  +vkWf++++ln++ n  ++++ +  ++ ai
  NCBI__GCF_003253485.1:WP_111394621.1   9 SGYLYEYQKSVAQPEEFWARIAD-SFHWRKRWNKVLKWNFEGpEVKWFDGATLNITENIFEKQLYTIGERPAI 80 
                                           56777899**************9.6***************988****************************** PP

                             TIGR02188  77 iwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfs 149
                                           iwe +e++e +r+ltY++l+revcr+an+lk+ G+ kgdrv+iY+pm+pea+iamlacaRiGa+hsvvfaGfs
  NCBI__GCF_003253485.1:WP_111394621.1  81 IWEPNEPDEPARTLTYRQLFREVCRFANALKAKGIGKGDRVIIYMPMVPEAAIAMLACARIGAIHSVVFAGFS 153
                                           ************************************************************************* PP

                             TIGR02188 150 aealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweel 222
                                           +++la+Ri+d++ak v+t+d+++Rg+k+i++k +vdealek++  ve+v+v+krtg+e ++++ grD+ww+e+
  NCBI__GCF_003253485.1:WP_111394621.1 154 SSSLADRINDCQAKAVLTSDGNFRGNKKITVKGVVDEALEKSS--VETVIVYKRTGQE-TTMVPGRDFWWDEV 223
                                           ****************************************985..*************.56************ PP

                             TIGR02188 223 vekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtG 295
                                           +e ++s+e  +e+++sed+lfiLYtsGstGkPkGv+httgGy+++++++++ vf++ ++d++wCtaDvGW+tG
  NCBI__GCF_003253485.1:WP_111394621.1 224 LE-GQSDENIAEEMESEDMLFILYTSGSTGKPKGVVHTTGGYMVYTKYSFENVFQYSPGDVYWCTADVGWITG 295
                                           **.69******************************************************************** PP

                             TIGR02188 296 hsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgs 368
                                           hsYivygPL++Gattl+fegvptyp++srfw+viek++v++fYtaPtaiRal++ g+e ++ +dlssl+vlgs
  NCBI__GCF_003253485.1:WP_111394621.1 296 HSYIVYGPLLAGATTLMFEGVPTYPNPSRFWQVIEKHQVNVFYTAPTAIRALQAFGTEPIEGYDLSSLKVLGS 368
                                           ************************************************************************* PP

                             TIGR02188 369 vGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeve 441
                                           vGepin eaw+Wy++++Gk++cpivdtwWqtetGgil++pl+g +t++kp+ atlPl+Gi+  +vd eg+e++
  NCBI__GCF_003253485.1:WP_111394621.1 369 VGEPINEEAWHWYHTHIGKGHCPIVDTWWQTETGGILVSPLAG-ITPTKPAYATLPLPGIQLCIVDAEGNELT 440
                                           *******************************************.5**************************** PP

                             TIGR02188 442 eeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgt 514
                                            ++ +g L+ik pwPsm+rt ygd+er  +tYf+++k++yftGDg++rd+dGy+ ilGRvDdvinvsGhr+gt
  NCBI__GCF_003253485.1:WP_111394621.1 441 GNSVEGNLCIKFPWPSMIRTTYGDHERCKQTYFSTYKNMYFTGDGVKRDHDGYYRILGRVDDVINVSGHRMGT 513
                                           777779******************************************************************* PP

                             TIGR02188 515 aeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvvee 587
                                           ae+e+a+ +h++v e+avvg+p+e+kg+ i+a+v+   +++++e +l +e+k++v+k igpiakpdki++v+ 
  NCBI__GCF_003253485.1:WP_111394621.1 514 AEVENAINEHPKVIESAVVGYPHEVKGQGIYAYVICDMTNRTEE-NLINEIKEMVSKIIGPIAKPDKIQIVPG 585
                                           ************************************99998888.5*************************** PP

                             TIGR02188 588 lPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           lPktRsGkimRR+lrk+aeg+ +++gd+stl dp+vve+++e
  NCBI__GCF_003253485.1:WP_111394621.1 586 LPKTRSGKIMRRILRKVAEGStDSMGDTSTLLDPEVVEKIIE 627
                                           ********************999****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (630 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 21.47
//
[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