Alignments for a candidate for acs in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Pseudarthrobacter sulfonivorans Ar51

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_058930181.1 AU252_RS07515 acetate--CoA ligase

Query= SwissProt::P9WQD1
         (651 letters)



>NCBI__GCF_001484605.1:WP_058930181.1
          Length = 738

 Score =  709 bits (1831), Expect = 0.0
 Identities = 361/655 (55%), Positives = 452/655 (69%), Gaps = 44/655 (6%)

Query: 9   SSSYPPPAHFAEHANARAELYREAEEDRLAFWAKQANRLSWTTP--FTEVLDWSGA---- 62
           +SS     H AEH          A+ D +AFW +QA RL W  P   +    W  A    
Sbjct: 80  TSSTTAAQHTAEH--------EAAQPDNVAFWEQQALRLDWAQPAGISGGKPWHTAHRRV 131

Query: 63  ---------PFAKWFVGGELNVAYNCVDRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLL 113
                    P   WF GG+LNVAYNCVDRHV  G GD VA H+EGEP GDRRT+TY++L 
Sbjct: 132 PADAAAGKGPEITWFEGGKLNVAYNCVDRHVANGRGDNVAFHFEGEP-GDRRTVTYAELQ 190

Query: 114 AEVSKAANALTDLGLVAGDRVAIYLPLIPEAVIAMLACARLGIMHSVVFGGFTAAALQAR 173
            EVSKAANAL  LG+  GDRV IYLP+IPE VI  LA AR+G +HS+VFGGF+A AL+ R
Sbjct: 191 REVSKAANALLALGITKGDRVVIYLPVIPETVIITLAVARIGAIHSLVFGGFSADALKFR 250

Query: 174 IVDAQAKLLITADGQFRRGKPSPLKAAADEALAAIPDCSVEHVLVVRRTGIE-----MAW 228
           + D  AKLL+T DGQFRRG   P+K  AD A+A   D ++EHVLVV RT        +  
Sbjct: 251 VEDTGAKLLVTTDGQFRRGVAVPVKDNADAAVAG--DNAIEHVLVVNRTTAPEDLAAVPM 308

Query: 229 SEGRDLWWHHVVGSASPAHTPEPFDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTM 288
           +EGRD+WWH  VGSA+  H PE FD+E PLF++YTSGTTGKPKG++HTSGGYLTQ  ++ 
Sbjct: 309 TEGRDVWWHDAVGSAADVHEPEAFDAETPLFIMYTSGTTGKPKGLVHTSGGYLTQASWSF 368

Query: 289 RTIFD----VKPDSDVFWCTADIGWVTGHTYGVYGPLCNGVTEVLYEGTPDTPDRHRHFQ 344
             +F        D DV WCTAD+ WVT HTY +YGPL NG T+V++EGTP+TP   RHF+
Sbjct: 369 EHLFSNPDPALRDQDVHWCTADLAWVTAHTYEIYGPLSNGATQVIFEGTPNTPHPGRHFE 428

Query: 345 IIEKYGVTIYYTAPTLIRMFMKWGRE-IPDSHDLSSLRLLGSVGEPINPEAWRWYRDVIG 403
           IIE+YGVT YYTAPTL+R  M W  + +PDS+DLSS+RLLG+VGE +NPEAWRW R  +G
Sbjct: 429 IIERYGVTQYYTAPTLVRSLMGWFPDGVPDSYDLSSIRLLGTVGEAVNPEAWRWLRQNVG 488

Query: 404 GGRTPLVDTWWQTETGSAMISPLPGIAAAKPGSAMTPLPGISAKIVDDHGDPLPPHTEGA 463
            G  P+VDTWWQ+ETG+ ++SP P     KPG A  PLPG+S +IVDD G+ +PP     
Sbjct: 489 AGTAPVVDTWWQSETGATILSPAPTDTEFKPGCAARPLPGVSTRIVDDAGNTVPPG---- 544

Query: 464 QHVTGYLVLDQPWPSMLRGIWGDPARYWHSYWSKFSDKGYYFAGDGARIDPDGAIWVLGR 523
             V G++V+D P P++ R +WG+P RY+ +YWSK+ ++G++ AGDGA+ D DG IW+LGR
Sbjct: 545 --VQGFIVVDTPGPAIARTVWGNPRRYYDAYWSKYVEQGWFLAGDGAKYDADGDIWILGR 602

Query: 524 IDDVMNVSGHRISTAEVESALVAHSGVAEAAVVGVTDETTTQAICAFVVLRANYAPHDRT 583
           +DD +NVSGH +ST E+ESALV+H+ V EA V  V D TT  AI AFVVL+   +     
Sbjct: 603 VDDTLNVSGHLLSTIEIESALVSHADVVEAGVCPVADPTTGHAIVAFVVLKRGVS--REV 660

Query: 584 AEELRTEVARVISPIARPRDVHVVPELPKTRSGKIMRRLLRDVAENRELGDTSTL 638
           A ELR  VA+ I PIA+PRDV VVP++PKTRSGKIMRRLL  + E   LGDT++L
Sbjct: 661 ATELRNHVAKAIGPIAKPRDVVVVPDVPKTRSGKIMRRLLTQLFEGTALGDTTSL 715


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: 1668
Number of extensions: 95
Number of successful extensions: 9
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: 738
Length adjustment: 39
Effective length of query: 612
Effective length of database: 699
Effective search space:   427788
Effective search space used:   427788
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_058930181.1 AU252_RS07515 (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.729630.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.1e-238  776.5   0.0   1.2e-237  776.1   0.0    1.1  1  NCBI__GCF_001484605.1:WP_058930181.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001484605.1:WP_058930181.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  776.1   0.0  1.2e-237  1.2e-237       6     627 ..      87     725 ..      82     727 .. 0.92

  Alignments for each domain:
  == domain 1  score: 776.1 bits;  conditional E-value: 1.2e-237
                             TIGR02188   6 eykelyeeaiedpekfwaklakeelewl........kpfekvldeslep.......kvkWfedgelnvsyncv 63 
                                           ++++ +e a+ d  +fw+++a + l+w+        kp+++  +   ++       +++Wfe+g+lnv+yncv
  NCBI__GCF_001484605.1:WP_058930181.1  87 QHTAEHEAAQPDNVAFWEQQALR-LDWAqpagisggKPWHTAHRRVPADaaagkgpEITWFEGGKLNVAYNCV 158
                                           56667888999999*******95.999833333333467766543211111234569**************** PP

                             TIGR02188  64 drhvek.rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlaca 135
                                           drhv++ r d+va ++eg+ +g d+r++tYael+rev+++an+l +lG+ kgdrv+iYlp+ipe+vi+ la+a
  NCBI__GCF_001484605.1:WP_058930181.1 159 DRHVANgRGDNVAFHFEGE-PG-DRRTVTYAELQREVSKAANALLALGITKGDRVVIYLPVIPETVIITLAVA 229
                                           *******************.77.59************************************************ PP

                             TIGR02188 136 RiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgee. 207
                                           RiGa+hs+vf+Gfsa+al+ R++d+ akl++t+d+++R+g ++++k+++d+a++  + ++e+vlvv+rt ++ 
  NCBI__GCF_001484605.1:WP_058930181.1 230 RIGAIHSLVFGGFSADALKFRVEDTGAKLLVTTDGQFRRGVAVPVKDNADAAVAGDN-AIEHVLVVNRTTAPe 301
                                           ******************************************************887.8*********98652 PP

                             TIGR02188 208 ...vaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfd 277
                                               ++++egrDvww+++v + a + +epe++d+e plfi+YtsG+tGkPkG++ht+gGyl++a+ +++ +f 
  NCBI__GCF_001484605.1:WP_058930181.1 302 dlaAVPMTEGRDVWWHDAVGS-AADVHEPEAFDAETPLFIMYTSGTTGKPKGLVHTSGGYLTQASWSFEHLFS 373
                                           222468**************6.9*************************************************6 PP

                             TIGR02188 278 .....ikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiR 345
                                                ++d+d++wCtaD+ Wvt h+Y +ygPL+nGat+++feg+p++p+++r++e+ie+y+vt++YtaPt++R
  NCBI__GCF_001484605.1:WP_058930181.1 374 npdpaLRDQDVHWCTADLAWVTAHTYEIYGPLSNGATQVIFEGTPNTPHPGRHFEIIERYGVTQYYTAPTLVR 446
                                           33344699***************************************************************** PP

                             TIGR02188 346 almkl.geelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelk 417
                                           +lm +  + +++++dlss+r+lg+vGe +npeaw+W++++vG + +p+vdtwWq etG+++++p p+  te k
  NCBI__GCF_001484605.1:WP_058930181.1 447 SLMGWfPDGVPDSYDLSSIRLLGTVGEAVNPEAWRWLRQNVGAGTAPVVDTWWQSETGATILSPAPT-DTEFK 518
                                           ***983577899*******************************************************.5**** PP

                             TIGR02188 418 pgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgar 488
                                           pg+a++Pl+G+++++vd+ g++v ++ + g++v+++p P+++rt++g+++r+ ++Y++k+ +   +++GDga+
  NCBI__GCF_001484605.1:WP_058930181.1 519 PGCAARPLPGVSTRIVDDAGNTVPPGVQ-GFIVVDTPGPAIARTVWGNPRRYYDAYWSKYVEqgWFLAGDGAK 590
                                           ***************************9.8*****************************976669******** PP

                             TIGR02188 489 rdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeel 561
                                            d+dG+iwilGRvDd +nvsGh l+t+eiesalvsh +v ea v  v+d ++g+aivafvvlk+gv+ +   +
  NCBI__GCF_001484605.1:WP_058930181.1 591 YDADGDIWILGRVDDTLNVSGHLLSTIEIESALVSHADVVEAGVCPVADPTTGHAIVAFVVLKRGVSRE---V 660
                                           ****************************************************************99854...6 PP

                             TIGR02188 562 ekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627
                                           ++el+++v+k igpiakp+++ vv+++PktRsGkimRRll ++ eg  +lgd++ l+++ +++ ++
  NCBI__GCF_001484605.1:WP_058930181.1 661 ATELRNHVAKAIGPIAKPRDVVVVPDVPKTRSGKIMRRLLTQLFEGT-ALGDTTSLQNEPAIAGIQ 725
                                           8*******************************************976.567*******99988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (738 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: 42.76
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 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