Alignments for a candidate for acs in Desulfovibrio oxyclinae DSM 11498

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Desulfovibrio oxyclinae DSM 11498

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_018125632.1 B149_RS0113155 acetate--CoA ligase

Query= BRENDA::Q2XNL6
         (634 letters)



>NCBI__GCF_000375485.1:WP_018125632.1
          Length = 639

 Score =  746 bits (1925), Expect = 0.0
 Identities = 356/632 (56%), Positives = 479/632 (75%), Gaps = 9/632 (1%)

Query: 8   LLEEKRVFKPHYTVVEEAHIKNWE---AELEKGKDHENYWAEKAERLEWFRKWDRVLDES 64
           LL+E+RVF+P   +V EA++   E   A  +   D   YW E A+ L+WF++WDRVLD+S
Sbjct: 10  LLQEERVFRPLPQLVIEANVNPQELGAARRQSEYDPLGYWEEAADELDWFKRWDRVLDDS 69

Query: 65  NRPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVSRTAN 124
            +PFYRWF   + N+ YN +DR ++T  +N++A+++  E GD RK TY+ELYREV+R AN
Sbjct: 70  RKPFYRWFPGARCNIVYNCLDRHIETANKNKLALIWEGEPGDSRKYTYFELYREVNRFAN 129

Query: 125 ALKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAKI 184
           AL++LG++KGD V +Y+P  PE VV+MLA AKIGAVHSV+++G S  AL +R+NDA+AK 
Sbjct: 130 ALRTLGVQKGDRVVVYMPPLPETVVAMLAAAKIGAVHSVVFAGFSAKALRQRINDAQAKA 189

Query: 185 IITADGTYRRGGVIKLKPIVDEAILQC--PTIETTVVVKHTDIDIEMSDISGREMLFDKL 242
           +ITADG YR G V++LK  VDEA++      +E+ VVV+ T + ++M D  GR+  ++ L
Sbjct: 190 VITADGFYRNGQVLRLKDTVDEALVGACADCVESMVVVRRTKVGVDMVD--GRDFWYEDL 247

Query: 243 IEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHNGDL 302
           +  E +    E M+A +PLF++YTSG+TGKPKG++H  GGYMVGV  TL   FD+   D+
Sbjct: 248 VRQERNTAPTEVMEAHEPLFLMYTSGTTGKPKGIVHCHGGYMVGVHRTLTTVFDVKPTDI 307

Query: 303 WWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTAPTA 362
           +WCTAD GW+TGHS VVYGPLL GTTT++YEG P+YP     W+IV KYG++ FYT PT 
Sbjct: 308 FWCTADPGWVTGHSAVVYGPLLAGTTTVIYEGHPNYPQADRLWNIVAKYGISIFYTVPTV 367

Query: 363 IRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTETGM 422
           IR LMRFG +H KR++L SL++LG+VGEPI+PEAW W Y+NIGR +CP+IDTWWQTETGM
Sbjct: 368 IRMLMRFGVQHTKRHDLSSLRLLGSVGEPISPEAWTWLYKNIGRSECPVIDTWWQTETGM 427

Query: 423 HLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLFNDE 482
            +I+PLP++ LKPGSVTKPLPG++ADVVD  G+ V  GKGG LVIR+PWPAM   L+NDE
Sbjct: 428 FMISPLPISLLKPGSVTKPLPGVKADVVDREGNSVEPGKGGLLVIREPWPAMMTGLWNDE 487

Query: 483 QRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFVAHP 542
            RY + Y++++P G Y AGD+AR+DEDGY WIQGR+DDV+NIAGHR+G+AE+E+ F AH 
Sbjct: 488 DRYRE-YFEKVP-GCYFAGDVARRDEDGYIWIQGRADDVINIAGHRVGSAELEAAFGAHR 545

Query: 543 AVAEAAVIGKADPIKGEVIKAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMVQVD 602
            V EAAVIG  D IKGE  KAF++++ G + +  LI++LKRH+R+ELGPVAV+  +    
Sbjct: 546 NVTEAAVIGVPDTIKGEAAKAFVVVRSGAEEDDELIKDLKRHIRNELGPVAVLKSIEFRR 605

Query: 603 SLPKTRSGKIMRRILRAREEGEDLGDTSTLEE 634
            LPKTRSGKIMRR+L+A E G ++GD + +E+
Sbjct: 606 KLPKTRSGKIMRRVLKAEETGTEIGDLTGMED 637


Lambda     K      H
   0.319    0.138    0.428 

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: 1248
Number of extensions: 55
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: 634
Length of database: 639
Length adjustment: 38
Effective length of query: 596
Effective length of database: 601
Effective search space:   358196
Effective search space used:   358196
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_018125632.1 B149_RS0113155 (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.2012664.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-266  871.9   0.0   1.3e-266  871.7   0.0    1.0  1  NCBI__GCF_000375485.1:WP_018125632.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000375485.1:WP_018125632.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  871.7   0.0  1.3e-266  1.3e-266       8     620 ..      35     638 ..      28     639 .] 0.97

  Alignments for each domain:
  == domain 1  score: 871.7 bits;  conditional E-value: 1.3e-266
                             TIGR02188   8 kelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaiiwe 79 
                                            +  ++++ dp  +w++ a  el+w+k +++vld+s +p+++Wf +++ n+ ync+drh+e+ +k+k+a+iwe
  NCBI__GCF_000375485.1:WP_018125632.1  35 GAARRQSEYDPLGYWEEAAD-ELDWFKRWDRVLDDSRKPFYRWFPGARCNIVYNCLDRHIETaNKNKLALIWE 106
                                           567799**********9998.6****************************************9********** PP

                             TIGR02188  80 gdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaea 152
                                           g+ +g dsrk+tY el+rev+r+an+l++lGv+kgdrv++Y+p +pe+v+amla+a+iGavhsvvfaGfsa+a
  NCBI__GCF_000375485.1:WP_018125632.1 107 GE-PG-DSRKYTYFELYREVNRFANALRTLGVQKGDRVVVYMPPLPETVVAMLAAAKIGAVHSVVFAGFSAKA 177
                                           **.77.59***************************************************************** PP

                             TIGR02188 153 laeRivdaeaklvitadeglRggkvielkkivdealek.aeesvekvlvvkrtgeevaewkegrDvwweelve 224
                                           l++Ri+da+ak vitad+ +R+g+v++lk++vdeal   + + ve+++vv+rt+  v  +++grD+w+e+lv+
  NCBI__GCF_000375485.1:WP_018125632.1 178 LRQRINDAQAKAVITADGFYRNGQVLRLKDTVDEALVGaCADCVESMVVVRRTKVGVD-MVDGRDFWYEDLVR 249
                                           ***********************************97515569*************66.************** PP

                             TIGR02188 225 keasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhs 297
                                           + ++++ ++e +++ +plf++YtsG+tGkPkG++h+ gGy++ ++ t  +vfd+k++difwCtaD GWvtGhs
  NCBI__GCF_000375485.1:WP_018125632.1 250 Q-ERNTAPTEVMEAHEPLFLMYTSGTTGKPKGIVHCHGGYMVGVHRTLTTVFDVKPTDIFWCTADPGWVTGHS 321
                                           6.9999******************************************************************* PP

                             TIGR02188 298 YivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvG 370
                                            +vygPL++G tt+++eg p+yp+a+r+w+++ ky+++ifYt Pt+iR+lm+ g +++k+hdlsslr+lgsvG
  NCBI__GCF_000375485.1:WP_018125632.1 322 AVVYGPLLAGTTTVIYEGHPNYPQADRLWNIVAKYGISIFYTVPTVIRMLMRFGVQHTKRHDLSSLRLLGSVG 394
                                           ************************************************************************* PP

                             TIGR02188 371 epinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveee 443
                                           epi peaw+W+y+++G+++cp++dtwWqtetG ++i+plp     lkpgs t+Pl+G++a+vvd+eg++ve++
  NCBI__GCF_000375485.1:WP_018125632.1 395 EPISPEAWTWLYKNIGRSECPVIDTWWQTETGMFMISPLPI--SLLKPGSVTKPLPGVKADVVDREGNSVEPG 465
                                           ****************************************8..589**************************9 PP

                             TIGR02188 444 eeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtae 516
                                           ++ g+Lvi++pwP+m+ ++++de+r+ e Yf+k++g+yf+GD arrd+dGyiwi+GR+Ddvin++Ghr+g+ae
  NCBI__GCF_000375485.1:WP_018125632.1 466 KG-GLLVIREPWPAMMTGLWNDEDRYRE-YFEKVPGCYFAGDVARRDEDGYIWIQGRADDVINIAGHRVGSAE 536
                                           99.8**********************75.9******************************************* PP

                             TIGR02188 517 iesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelP 589
                                           +e+a+ +h +v+eaav+gvpd+ikgea  afvv+++g+eed+e l k+lk+++r+e+gp+a  ++i++ ++lP
  NCBI__GCF_000375485.1:WP_018125632.1 537 LEAAFGAHRNVTEAAVIGVPDTIKGEAAKAFVVVRSGAEEDDE-LIKDLKRHIRNELGPVAVLKSIEFRRKLP 608
                                           ***************************************9995.***************************** PP

                             TIGR02188 590 ktRsGkimRRllrkiaegeellgdvstledp 620
                                           ktRsGkimRR+l++  +g  ++gd++ +ed+
  NCBI__GCF_000375485.1:WP_018125632.1 609 KTRSGKIMRRVLKAEETGT-EIGDLTGMEDD 638
                                           ************9876665.566**999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (639 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 0.03s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 9.50
//
[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