Alignments for a candidate for acs in Algoriphagus machipongonensis PR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Algoriphagus machipongonensis PR1

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_008198284.1 ALPR1_RS02860 acetate--CoA ligase

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



>NCBI__GCF_000166275.1:WP_008198284.1
          Length = 630

 Score =  722 bits (1864), Expect = 0.0
 Identities = 358/625 (57%), Positives = 443/625 (70%), Gaps = 7/625 (1%)

Query: 24  YKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVDIKWFADGTLNVSYNCLD 83
           Y   YQ+SV  P+ FW   A    W K +    + +F+    D+KWF +G LN++ N  +
Sbjct: 11  YLHEYQKSVAQPEEFWARIADSFHWRKRWDKTLKWNFEGP--DVKWFLNGKLNITENIFE 68

Query: 84  RHLAERGDQIAIIWEGDDPSES-RNITYRELHEEVCKFANALRGQDVHRGDVVTIYMPMI 142
           R+L   GD+ AIIWE +DP+E+ R +TYREL EEV +F+NAL+ + + +GD V IYMPM+
Sbjct: 69  RYLFTIGDRPAIIWEPNDPNEAGRTLTYRELFEEVSRFSNALKSKGIGKGDKVIIYMPMV 128

Query: 143 PEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITADEGVRAGKKIPLKANV 202
           PEA VAMLAC RIGAIHSVVF GFS  ALA RI DC++K V+T+D   R  KKI +KA V
Sbjct: 129 PEAAVAMLACARIGAIHSVVFAGFSSNALADRINDCEAKAVLTSDGNFRGSKKIAVKAVV 188

Query: 203 DDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAGTVCAPKEMGAEEALFIL 262
           D+ALT    SS++ VIV +RT  ++     RD W+ D++      C  +EM +E+ LFIL
Sbjct: 189 DEALTK---SSVETVIVYQRTHQDVTMQDGRDYWWHDVVADESKDCPAEEMDSEDMLFIL 245

Query: 263 YTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTADVGWVTGHSYIVYGPLA 322
           YTSGSTGKPKGV HTT GY++Y+  + E VF Y PG+VYWCTADVGW+TGHSYIVYGPL 
Sbjct: 246 YTSGSTGKPKGVVHTTGGYMVYSKYSFENVFQYSPGDVYWCTADVGWITGHSYIVYGPLL 305

Query: 323 NGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMMASGTAAVEGADGSSLRL 382
            GATT++FEGVP +PD  R   +++K+KV+  YTAPTAIRA+ A GT  +E  D SSL++
Sbjct: 306 AGATTIMFEGVPTFPDCGRFWAIVEKYKVNQFYTAPTAIRALQAYGTVEIEKYDLSSLKV 365

Query: 383 LGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISPLPGATALKPGSATRPFF 442
           LGSVGEPIN EAW WY+ ++GK +CPIVDTWWQTETGG+++SP+ G T  KP  AT P  
Sbjct: 366 LGSVGEPINEEAWHWYHTHIGKNKCPIVDTWWQTETGGIMVSPIAGITPTKPAYATLPLP 425

Query: 443 GVVPALVDNLGNLIEG-AAEGNLVILDSWPGQARTLYGDHDRFVDTYFKTFSGMYFTGDG 501
           GV   +VD  GN + G + EGNL I   WP   RT YGDHDR   TYF T+ GMYFTGDG
Sbjct: 426 GVQLCIVDPEGNELTGNSVEGNLCIKFPWPSMIRTTYGDHDRCKQTYFSTYKGMYFTGDG 485

Query: 502 ARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAAVVGVPHDIKGQGIYV 561
            +RD DGYY I GRVDDV+NVSGHRMGTAE+E+A+  HPKV E+AVVG PHD+KGQGIY 
Sbjct: 486 VKRDHDGYYRILGRVDDVINVSGHRMGTAEVENAINEHPKVIESAVVGYPHDVKGQGIYA 545

Query: 562 YVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIATA 621
           YV  +    T + L  E+K  V K IGPIA PD IQ  PGLPKTRSGKIMRRILRK+A  
Sbjct: 546 YVICDLTNRTEDNLVNEIKEMVSKIIGPIAKPDKIQLVPGLPKTRSGKIMRRILRKVAEN 605

Query: 622 EYDGLGDISTLADPGVVAHLIETHK 646
             D +GD STL DP VV  +I+  K
Sbjct: 606 NLDNMGDTSTLLDPDVVEKIIDGRK 630


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: 1272
Number of extensions: 68
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: 651
Length of database: 630
Length adjustment: 38
Effective length of query: 613
Effective length of database: 592
Effective search space:   362896
Effective search space used:   362896
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_008198284.1 ALPR1_RS02860 (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.3908404.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-294  963.8   0.8     2e-294  963.6   0.8    1.0  1  NCBI__GCF_000166275.1:WP_008198284.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166275.1:WP_008198284.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  963.6   0.8    2e-294    2e-294       4     627 ..       8     626 ..       5     628 .. 0.98

  Alignments for each domain:
  == domain 1  score: 963.6 bits;  conditional E-value: 2e-294
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkva 75 
                                           l+ y + y++++++pe+fwa+ a  +++w k ++k+l++++e  +vkWf +g+ln++ n  +r++ +  d+ a
  NCBI__GCF_000166275.1:WP_008198284.1   8 LSGYLHEYQKSVAQPEEFWARIAD-SFHWRKRWDKTLKWNFEGpDVKWFLNGKLNITENIFERYLFTIGDRPA 79 
                                           6678899****************9.6***************988***************************** PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           iiwe ++++e  r+ltY+el++ev+r++n+lk+ G+ kgd+v+iY+pm+pea++amlacaRiGa+hsvvfaGf
  NCBI__GCF_000166275.1:WP_008198284.1  80 IIWEPNDPNEAGRTLTYRELFEEVSRFSNALKSKGIGKGDKVIIYMPMVPEAAVAMLACARIGAIHSVVFAGF 152
                                           ************************************************************************* PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221
                                           s++ala+Ri+d+eak v+t+d+++Rg k+i++k++vdeal+k+  sve+v+v++rt ++v+ +++grD+ww++
  NCBI__GCF_000166275.1:WP_008198284.1 153 SSNALADRINDCEAKAVLTSDGNFRGSKKIAVKAVVDEALTKS--SVETVIVYQRTHQDVT-MQDGRDYWWHD 222
                                           *****************************************98..5*************76.*********** PP

                             TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvt 294
                                           +v++ +s++c++e++dsed+lfiLYtsGstGkPkGv+httgGy+++ +++++ vf++ ++d++wCtaDvGW+t
  NCBI__GCF_000166275.1:WP_008198284.1 223 VVAD-ESKDCPAEEMDSEDMLFILYTSGSTGKPKGVVHTTGGYMVYSKYSFENVFQYSPGDVYWCTADVGWIT 294
                                           ***7.******************************************************************** PP

                             TIGR02188 295 GhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlg 367
                                           GhsYivygPL++Gatt++fegvpt+pd +rfw+++ekykv++fYtaPtaiRal+++g+  ++k+dlssl+vlg
  NCBI__GCF_000166275.1:WP_008198284.1 295 GHSYIVYGPLLAGATTIMFEGVPTFPDCGRFWAIVEKYKVNQFYTAPTAIRALQAYGTVEIEKYDLSSLKVLG 367
                                           ************************************************************************* PP

                             TIGR02188 368 svGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkev 440
                                           svGepin eaw+Wy++++Gk+kcpivdtwWqtetGgi+++p++g +t++kp+ atlPl+G++  +vd eg+e+
  NCBI__GCF_000166275.1:WP_008198284.1 368 SVGEPINEEAWHWYHTHIGKNKCPIVDTWWQTETGGIMVSPIAG-ITPTKPAYATLPLPGVQLCIVDPEGNEL 439
                                           ********************************************.5*************************** PP

                             TIGR02188 441 eeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlg 513
                                           + ++ +g L+ik pwPsm+rt ygd++r  +tYf+++kg+yftGDg++rd+dGy+ ilGRvDdvinvsGhr+g
  NCBI__GCF_000166275.1:WP_008198284.1 440 TGNSVEGNLCIKFPWPSMIRTTYGDHDRCKQTYFSTYKGMYFTGDGVKRDHDGYYRILGRVDDVINVSGHRMG 512
                                           *777779****************************************************************** PP

                             TIGR02188 514 taeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvve 586
                                           tae+e+a+ +h++v e+avvg+p+++kg+ i+a+v+   ++++++ +l +e+k++v+k igpiakpdki++v+
  NCBI__GCF_000166275.1:WP_008198284.1 513 TAEVENAINEHPKVIESAVVGYPHDVKGQGIYAYVICDLTNRTED-NLVNEIKEMVSKIIGPIAKPDKIQLVP 584
                                           *************************************99999888.5************************** PP

                             TIGR02188 587 elPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627
                                            lPktRsGkimRR+lrk+ae++ +++gd+stl dp vve+++
  NCBI__GCF_000166275.1:WP_008198284.1 585 GLPKTRSGKIMRRILRKVAENNlDNMGDTSTLLDPDVVEKII 626
                                           ****************************************97 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 20.40
//
[ok]

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

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Protein sequences (fasta format)
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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