Alignments for a candidate for acs in Kocuria flava HO-9041

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Kocuria flava HO-9041

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_147050318.1 AS188_RS14775 acetate--CoA ligase

Query= SwissProt::P9WQD1
         (651 letters)



>NCBI__GCF_001482365.1:WP_147050318.1
          Length = 649

 Score =  840 bits (2171), Expect = 0.0
 Identities = 414/651 (63%), Positives = 500/651 (76%), Gaps = 15/651 (2%)

Query: 2   SESTPEVSSSYPPPAHFAEHANARAELYREAEEDRLAFWAKQANRL-SWTTPFTEVLDWS 60
           SE+ P  ++++ P   FA  ANA AELY +AE +   FWA+QA  L +W+  FTEVLDWS
Sbjct: 3   SETAPVETTTFAPSREFAAQANAGAELYEQAEAEGTEFWARQARELLTWSKDFTEVLDWS 62

Query: 61  GAPFAKWFVGGELNVAYNCVDRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLLAEVSKAA 120
             PFAKWF  G LN  YN VDRHVEAG+GDRVAIH+EGEP GD R+ TY++L  EVSKAA
Sbjct: 63  NPPFAKWFQDGTLNACYNAVDRHVEAGNGDRVAIHFEGEP-GDSRSYTYAELKDEVSKAA 121

Query: 121 NALTDLGLVAGDRVAIYLPLIPEAVIAMLACARLGIMHSVVFGGFTAAALQARIVDAQAK 180
           NA+ DLG+V GDRVA+YLP+IPEAVIAMLACAR+G +HSVVFGGF+A AL++R+ D QAK
Sbjct: 122 NAMADLGVVKGDRVALYLPMIPEAVIAMLACARIGAIHSVVFGGFSADALRSRVEDGQAK 181

Query: 181 LLITADGQFRRGKPSPLKAAADEALAAIPDCSVEHVLVVRRTGIEMAWSEGRDLWWHHVV 240
           L++TADG FRRGKPS LK A D+AL+     SVEHVLVVRR   E+  +EGRD+WWH VV
Sbjct: 182 LVVTADGSFRRGKPSMLKPAVDDALSR-GGSSVEHVLVVRRNEAEVGMTEGRDVWWHDVV 240

Query: 241 GSASPAHTPEPFDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTMRTIFDVKPDSDV 300
            +AS  HTP    +E PLF+LYTSGTTGKPKGIMHT+GGYLTQ  +T + +FD+KP +DV
Sbjct: 241 DAASTEHTPSEQGAEDPLFVLYTSGTTGKPKGIMHTTGGYLTQGAFTHKYVFDLKPKTDV 300

Query: 301 FWCTADIGWVTGHTYGVYGPLCNGVTEVLYEGTPDTPDRHRHFQIIEKYGVTIYYTAPTL 360
           +WCTAD+GWVTGH+Y  Y PL NG T+V+YEGTPD+P R R ++I++KY V+I YT+PT 
Sbjct: 301 YWCTADVGWVTGHSYVAYAPLVNGSTQVIYEGTPDSPHRGRFWEIVQKYKVSIMYTSPTA 360

Query: 361 IRMFMKWGREIPDSHDLSSLRLLGSVGEPINPEAWRWYRDVIGGGRTPLVDTWWQTETGS 420
           IR  MKWG EIP  +DLSSLR+LG+VGE INPEAW W+  VIGGGR P+VDTWWQTETG+
Sbjct: 361 IRTMMKWGEEIPAEYDLSSLRVLGTVGEAINPEAWTWFHRVIGGGRCPIVDTWWQTETGA 420

Query: 421 AMISPLPGIAAAKPGSAMTPLPGISAKIVDDHGDPLPPHTEGAQHVTGYLVLDQPWPSML 480
            MIS LPG+  AKPGSA  P+PGI   +VDD G PL          +G LV+ +PWP+ML
Sbjct: 421 IMISQLPGVTVAKPGSAQVPMPGIKVDVVDDEGKPL------GNEQSGLLVVREPWPAML 474

Query: 481 RGIWGDPARYWHSYWSKFSDKGYYFAGDGARIDPDGAIWVLGRIDDVMNVSGHRISTAEV 540
           R IWGD  RY  +YWS+F D   YFAGDGA+ D DG +W+LGR+DDVMNVSGHR+ST E+
Sbjct: 475 RTIWGDDDRYVDTYWSRFGD--MYFAGDGAKRDADGDVWILGRVDDVMNVSGHRLSTPEI 532

Query: 541 ESALVAHSGVAEAAVVGVTDETTTQAICAFVVL--RANYAPHDRT--AEELRTEVARVIS 596
           ESALV+HS VAEAAVVG TDETT QA+ AFV+L  +A     D+   AEE+R  V + IS
Sbjct: 533 ESALVSHSSVAEAAVVGATDETTGQAVIAFVILSDQAEAEGRDKAELAEEMRAHVGKEIS 592

Query: 597 PIARPRDVHVVPELPKTRSGKIMRRLLRDVAENRELGDTSTLLDPTVFDAI 647
           PIA+P+ V +VPELPKTRSGKIMRRLL+DVAE RE+GD STL D TV   I
Sbjct: 593 PIAKPKKVLIVPELPKTRSGKIMRRLLKDVAEEREVGDVSTLADQTVMQQI 643


Lambda     K      H
   0.319    0.136    0.433 

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: 1430
Number of extensions: 72
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: 651
Length of database: 649
Length adjustment: 38
Effective length of query: 613
Effective length of database: 611
Effective search space:   374543
Effective search space used:   374543
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 (21.8 bits)
S2: 54 (25.4 bits)

Align candidate WP_147050318.1 AS188_RS14775 (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.517365.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-297  973.5   0.7   2.3e-297  973.3   0.7    1.0  1  NCBI__GCF_001482365.1:WP_147050318.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001482365.1:WP_147050318.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  973.3   0.7  2.3e-297  2.3e-297       4     627 ..      23     644 ..      20     646 .. 0.97

  Alignments for each domain:
  == domain 1  score: 973.3 bits;  conditional E-value: 2.3e-297
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkva 75 
                                           +++ +elye+a+++ ++fwa++a+e l+w k+f++vld+s++p++kWf+dg+ln++yn+vdrhve+ + d+va
  NCBI__GCF_001482365.1:WP_147050318.1  23 ANAGAELYEQAEAEGTEFWARQARELLTWSKDFTEVLDWSNPPFAKWFQDGTLNACYNAVDRHVEAgNGDRVA 95 
                                           667789******************************************************************* PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           i++eg+ +g dsr++tYael++ev+++an++ +lGv kgdrva+YlpmipeaviamlacaRiGa+hsvvf+Gf
  NCBI__GCF_001482365.1:WP_147050318.1  96 IHFEGE-PG-DSRSYTYAELKDEVSKAANAMADLGVVKGDRVALYLPMIPEAVIAMLACARIGAIHSVVFGGF 166
                                           ******.77.59************************************************************* PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221
                                           sa+al++R++d +aklv+tad+++R+gk  +lk +vd+al++  +sve+vlvv+r+++ev  ++egrDvww++
  NCBI__GCF_001482365.1:WP_147050318.1 167 SADALRSRVEDGQAKLVVTADGSFRRGKPSMLKPAVDDALSRGGSSVEHVLVVRRNEAEVG-MTEGRDVWWHD 238
                                           ***********************************************************76.*********** PP

                             TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdik.dedifwCtaDvGWv 293
                                           +v+  as+e++p + ++edplf+LYtsG+tGkPkG++httgGyl++ a t+kyvfd+k ++d++wCtaDvGWv
  NCBI__GCF_001482365.1:WP_147050318.1 239 VVDA-ASTEHTPSEQGAEDPLFVLYTSGTTGKPKGIMHTTGGYLTQGAFTHKYVFDLKpKTDVYWCTADVGWV 310
                                           ***5.*****************************************************557************ PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGhsY+ y+PL+nG t++++eg+p+ p+++rfwe+++kykv+i+Yt+PtaiR++mk+gee+++++dlsslrvl
  NCBI__GCF_001482365.1:WP_147050318.1 311 TGHSYVAYAPLVNGSTQVIYEGTPDSPHRGRFWEIVQKYKVSIMYTSPTAIRTMMKWGEEIPAEYDLSSLRVL 383
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           g+vGe inpeaw+W+++v+G ++cpivdtwWqtetG+i+i++lpg +t +kpgsa++P++Gi+++vvd+egk+
  NCBI__GCF_001482365.1:WP_147050318.1 384 GTVGEAINPEAWTWFHRVIGGGRCPIVDTWWQTETGAIMISQLPG-VTVAKPGSAQVPMPGIKVDVVDDEGKP 455
                                           *********************************************.5************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512
                                           + +e++ g+Lv+++pwP+mlrti+gd++r+v+tY++++ ++yf+GDga+rd+dG++wilGRvDdv+nvsGhrl
  NCBI__GCF_001482365.1:WP_147050318.1 456 LGNEQS-GLLVVREPWPAMLRTIWGDDDRYVDTYWSRFGDMYFAGDGAKRDADGDVWILGRVDDVMNVSGHRL 527
                                           ***999.8***************************************************************** PP

                             TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee...elekelkklvrkeigpiakpdki 582
                                           +t eiesalvsh++vaeaavvg++de++g+a++afv+l++++e++ +   el++e++++v kei+piakp+k+
  NCBI__GCF_001482365.1:WP_147050318.1 528 STPEIESALVSHSSVAEAAVVGATDETTGQAVIAFVILSDQAEAEGRdkaELAEEMRAHVGKEISPIAKPKKV 600
                                           ***************************************998855433459********************** PP

                             TIGR02188 583 lvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627
                                           l+v+elPktRsGkimRRll+++ae++e +gdvstl+d++v++++ 
  NCBI__GCF_001482365.1:WP_147050318.1 601 LIVPELPKTRSGKIMRRLLKDVAEERE-VGDVSTLADQTVMQQIV 644
                                           ***********************9665.67************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (649 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: 25.85
//
[ok]

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

Downloads

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

Related tools

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 2024 update 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