Alignments for a candidate for acs in Nautilia profundicola AmH

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Nautilia profundicola AmH

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_015902166.1 NAMH_RS04985 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000021725.1:WP_015902166.1
          Length = 651

 Score =  740 bits (1910), Expect = 0.0
 Identities = 367/646 (56%), Positives = 466/646 (72%), Gaps = 11/646 (1%)

Query: 13  VFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQSNAPF 72
           V+ P +      A  +M  Y  L +E E+DYEG WA+ ARE + W + F + LD SNAPF
Sbjct: 5   VYYPKKEMFKDPAFKNMCEYHELVEEFEKDYEGTWAKFAREKITWFEDFKQTLDTSNAPF 64

Query: 73  YKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFANGLKA 132
           YKWF  G+LN +Y C+DR+L+N   +K AI++E D+G    +TY EL+ +V RFAN LK+
Sbjct: 65  YKWFVGGKLNVAYQCIDRHLEN-RKNKAAIIWEGDNGEKRIITYLELYREVNRFANLLKS 123

Query: 133 LGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGAVALITA 192
           LG++KGDRVVIYMPM  E   AM ACAR+GA HSVVFGGFSA++L++R++D  A  +ITA
Sbjct: 124 LGVKKGDRVVIYMPMIPEAAFAMLACARIGAIHSVVFGGFSAEALKDRILDAEAKVVITA 183

Query: 193 DEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDVSAGQPD 252
           D   R G    LK   D  +AL G + V  VIV  R    + W  GRD    D+   Q D
Sbjct: 184 DGAFRKGSPYMLKPTVD--IALEGVDIVEKVIVVERNNEDIEWVSGRDISYNDLIVNQSD 241

Query: 253 TCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDLFWCTAD 312
            C AE + +E PLF+LYTSGSTGKPKGVQH+  GY+LWA +TM+W FDIK +D +WCTAD
Sbjct: 242 ECPAEIMDSEDPLFLLYTSGSTGKPKGVQHAQAGYILWAQLTMEWVFDIKDNDTYWCTAD 301

Query: 313 IGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIRSLIK 372
           IGW+TGHTYI YGPLAAGAT ++FEGV TYP++GR W M+  +KV+ FYTAPTAIR L K
Sbjct: 302 IGWITGHTYIVYGPLAAGATTLMFEGVLTYPDSGRAWKMVEEYKVNQFYTAPTAIRLLNK 361

Query: 373 AAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQTETGGHM 432
               +    PK+YDLSSLR+LGTVGEPI+P AW WYY+ +G  RC IVDT+WQTETGGHM
Sbjct: 362 MGPDE----PKKYDLSSLRILGTVGEPIDPPAWKWYYEVVGGGRCSIVDTWWQTETGGHM 417

Query: 433 ITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRTIWGDPE 492
           ITPLP ATP+ P S T PLPGI A I+DETG  +P    G+L + +PWP+MIRTIWGDPE
Sbjct: 418 ITPLPAATPVKPASATFPLPGIFAEIIDETGERMPAHEKGLLCITKPWPSMIRTIWGDPE 477

Query: 493 RFRKSYF--PEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESALV 550
           RF KSYF   +++G  +Y +GDG++ D+D GY  I GR+DDV+NVSGHR+GT EIE+A+ 
Sbjct: 478 RFVKSYFSTAKKMGEPVYFSGDGAMYDED-GYIWITGRVDDVINVSGHRLGTAEIEAAIK 536

Query: 551 SNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGPIAKPK 610
            +PL+AE AVVGRPD++ GE++ A+VVLK      EE ++I  E+   V +EIG IAK  
Sbjct: 537 KHPLIAEVAVVGRPDEIKGESVFAYVVLKGEDTVAEE-MEIIKEINEIVKEEIGAIAKVD 595

Query: 611 DIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQL 656
            + F   LPKTRSGKIMRR+LR++AKGE ITQDTSTLE+P ++E +
Sbjct: 596 TVAFVPGLPKTRSGKIMRRILRAIAKGEAITQDTSTLEDPKVVEAI 641


Lambda     K      H
   0.319    0.136    0.422 

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: 1258
Number of extensions: 61
Number of successful extensions: 7
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: 660
Length of database: 651
Length adjustment: 38
Effective length of query: 622
Effective length of database: 613
Effective search space:   381286
Effective search space used:   381286
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_015902166.1 NAMH_RS04985 (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.4083330.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     8e-306 1001.3   0.8   9.2e-306 1001.1   0.8    1.0  1  NCBI__GCF_000021725.1:WP_015902166.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000021725.1:WP_015902166.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1001.1   0.8  9.2e-306  9.2e-306       2     628 ..      19     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1001.1 bits;  conditional E-value: 9.2e-306
                             TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvekrkdkv 74 
                                           +++ ey+el+ee ++d+e  wak a+e+++w+++f+++ld+s++p++kWf++g+lnv+y+c+drh+e+rk+k+
  NCBI__GCF_000021725.1:WP_015902166.1  19 KNMCEYHELVEEFEKDYEGTWAKFAREKITWFEDFKQTLDTSNAPFYKWFVGGKLNVAYQCIDRHLENRKNKA 91 
                                           6789********************************************************************* PP

                             TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
                                           aiiwegd+   ++r +tY el+rev+r+an+lk+lGvkkgdrv+iY+pmipea++amlacaRiGa+hsvvf+G
  NCBI__GCF_000021725.1:WP_015902166.1  92 AIIWEGDNG--EKRIITYLELYREVNRFANLLKSLGVKKGDRVVIYMPMIPEAAFAMLACARIGAIHSVVFGG 162
                                           *******55..48************************************************************ PP

                             TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220
                                           fsaeal++Ri daeak+vitad+++R+g  ++lk +vd ale ++  vekv+vv+r++e+++ w++grD+ ++
  NCBI__GCF_000021725.1:WP_015902166.1 163 FSAEALKDRILDAEAKVVITADGAFRKGSPYMLKPTVDIALEGVD-IVEKVIVVERNNEDIE-WVSGRDISYN 233
                                           *******************************************98.7*************66.********** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           +l+  ++s+ec++e +dsedplf+LYtsGstGkPkGv+h+++Gy+l+a+lt+++vfdikd+d++wCtaD+GW+
  NCBI__GCF_000021725.1:WP_015902166.1 234 DLIV-NQSDECPAEIMDSEDPLFLLYTSGSTGKPKGVQHAQAGYILWAQLTMEWVFDIKDNDTYWCTADIGWI 305
                                           ****.5******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGh+YivygPLa+Gattl+fegv typd++r w+++e+ykv++fYtaPtaiR+l k+g + +kk+dlsslr+l
  NCBI__GCF_000021725.1:WP_015902166.1 306 TGHTYIVYGPLAAGATTLMFEGVLTYPDSGRAWKMVEEYKVNQFYTAPTAIRLLNKMGPDEPKKYDLSSLRIL 378
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           g+vGepi+p aw+WyyevvG ++c+ivdtwWqtetGg++itplp+ at++kp+sat Pl+Gi ae++de+g++
  NCBI__GCF_000021725.1:WP_015902166.1 379 GTVGEPIDPPAWKWYYEVVGGGRCSIVDTWWQTETGGHMITPLPA-ATPVKPASATFPLPGIFAEIIDETGER 450
                                           *********************************************.6************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg....lyftGDgarrdkdGyiwilGRvDdvinvs 508
                                           + ++e+ g+L+i+kpwPsm+rti+gd+erfv++Yf+++k+    +yf+GDga+ d+dGyiwi+GRvDdvinvs
  NCBI__GCF_000021725.1:WP_015902166.1 451 MPAHEK-GLLCITKPWPSMIRTIWGDPERFVKSYFSTAKKmgepVYFSGDGAMYDEDGYIWITGRVDDVINVS 522
                                           ***999.8******************************9989999**************************** PP

                             TIGR02188 509 Ghrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee.elekelkklvrkeigpiakpd 580
                                           Ghrlgtaeie+a+ +h+ +ae avvg+pdeikge+++a+vvlk + +  ee e+ ke++++v++eig+iak d
  NCBI__GCF_000021725.1:WP_015902166.1 523 GHRLGTAEIEAAIKKHPLIAEVAVVGRPDEIKGESVFAYVVLKGEDTVAEEmEIIKEINEIVKEEIGAIAKVD 595
                                           *******************************************9988777669******************** PP

                             TIGR02188 581 kilvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelke 628
                                           ++ +v+ lPktRsGkimRR+lr+ia+ge +++d+stledp+vve+++e
  NCBI__GCF_000021725.1:WP_015902166.1 596 TVAFVPGLPKTRSGKIMRRILRAIAKGEAITQDTSTLEDPKVVEAIIE 643
                                           ********************************************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 26.63
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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