Alignments for a candidate for acs in Methanobacterium arcticum M2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Methanobacterium arcticum M2

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_048080955.1 EI99_RS05765 acetate--CoA ligase

Query= BRENDA::A0B8F1
         (659 letters)



>NCBI__GCF_000746075.1:WP_048080955.1
          Length = 650

 Score =  786 bits (2030), Expect = 0.0
 Identities = 374/648 (57%), Positives = 483/648 (74%), Gaps = 8/648 (1%)

Query: 8   AVLQEETRIFNTPQWIIEYSNSYQWMKKKGFKTEKEMREWCAQNYLDFWDEMAQTYADWF 67
           A+L+EE RIF   + I+E SN  QWM K   K   E+ +    N   FWD++A+   +WF
Sbjct: 7   ALLKEE-RIFKPTKDIVEKSNITQWMNKYKIKNYDELLKKANDNPDWFWDDLAKEL-EWF 64

Query: 68  KPYTQILEWNPPYAKWFLGGKCNVAHNAVDRHAKSWRRNKVAYYFVGEPVGDTKTITYYQ 127
           +PY  +L+W+PP+A+WFL GK N+AHNA+DRH K+ + +K+AY + GE  G T+ ITY+Q
Sbjct: 65  EPYKNVLKWDPPHAEWFLEGKFNIAHNALDRHIKNGKGDKIAYIWEGED-GKTRKITYHQ 123

Query: 128 LYQAVNKMANGLKSLGVKKGDRVSIYLPMIPELPITMLACAKIGAIHSVVFSGFSAGGLQ 187
           L+  VNK AN L+ LG+ KGD VSIYLPMIPELP+ MLACAKIGA+HSVVFSGF A   Q
Sbjct: 124 LWCDVNKFANALRELGIGKGDTVSIYLPMIPELPVAMLACAKIGAVHSVVFSGFWAKAFQ 183

Query: 188 SRVTDAEAKVVVTSDGFYRRGKPLPLKPNVDEAVQNAPSVEKVVVVKRVGLDVPMKEGRD 247
            RV D+++KV +T+DGF RRGK +PLK NVD+ +QN P+++ ++V+   G+DV M EGRD
Sbjct: 184 ERVNDSKSKVAITTDGFTRRGKLIPLKENVDDILQNTPTIKNLIVINNAGIDVKMHEGRD 243

Query: 248 IWYHDLVKDQPAECYTEELDPEDRLFILYTSGTTGKPKGIEHAHGGFCVGPAYTTAWALD 307
           +W+H++ ++   EC TE +D ED LFILYTSGTTGKPKG+ H HGG+ VG   T  +  D
Sbjct: 244 LWWHEITENMSEECETEVMDSEDPLFILYTSGTTGKPKGVVHVHGGYAVGIYTTLKFVFD 303

Query: 308 VHEEDVYWCTADCGWITGHSYVVYGPLCLGATSILYEGAPDYPDIGRWWSIIEEYGVSVF 367
           ++E+D++WC AD GWITGHSY+VY PL LG TSI++EG PDYPD GR W I+E Y V+VF
Sbjct: 304 LNEDDIWWCAADIGWITGHSYIVYAPLLLGVTSIIFEGTPDYPDPGRLWKIVEGYKVNVF 363

Query: 368 YTAPTAIRMFMKAGDQWPKKYNLKSIRILASVGEPLNPEAYVWFRNNIGGGQAPIIDTWW 427
           YTAPT IRMFMK G +WP+KY+L SIR+L SVGEP+NPEA+VW+   IG  + PI+DTWW
Sbjct: 364 YTAPTTIRMFMKYGPKWPQKYDLSSIRLLGSVGEPINPEAWVWYYKYIGREKCPIMDTWW 423

Query: 428 QTETGCHVIAPLPMTPEKPGSVAFPLPGFNTDIYDEDGNSVPLGYGGNIVQKTPWPSMLR 487
           QTETG H+I PLP++P KPGS   P P    DI D+ G S+    GG++V KTPWPSMLR
Sbjct: 424 QTETGMHLITPLPISPLKPGSAVMPFPTVQADILDDMGRSL-TEKGGHLVIKTPWPSMLR 482

Query: 488 AFFRDPERYMKEYWQMYWDIKPGTYLAGDKATRDKDGYWWIQGRIDDVLKVAGHRISNAE 547
             +R+P+RY+K YW  + ++    YL+GD A +D DGY+WIQGR DDVL VAGHRI  AE
Sbjct: 483 TIYRNPQRYIKTYWSAFKNM----YLSGDVARKDSDGYFWIQGREDDVLSVAGHRIGTAE 538

Query: 548 VESAAVSHPAVAEAAVIGKPDEVKGEVIVAFIILKEGVQESEDLKKDIAKHVRSVLGPVA 607
           VESA VS+  VAEAAV+GKPDE+KGE I AF+ILK+  + +++LK  +  HVR  +GPVA
Sbjct: 539 VESALVSYECVAEAAVVGKPDEIKGEEIAAFVILKDNFKPTQELKDTLKYHVRVEIGPVA 598

Query: 608 YPEIVYFVKDVPKTRSGKIMRRVIKAKALGKPVGDISALANPESVENI 655
            P+ + FV D+PKTRSGKIMRRVIKAK  G+ VGD S LANPE+V+ +
Sbjct: 599 TPKYISFVDDLPKTRSGKIMRRVIKAKVKGEDVGDTSTLANPEAVDGL 646


Lambda     K      H
   0.318    0.137    0.438 

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: 1425
Number of extensions: 59
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: 659
Length of database: 650
Length adjustment: 38
Effective length of query: 621
Effective length of database: 612
Effective search space:   380052
Effective search space used:   380052
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_048080955.1 EI99_RS05765 (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.3495243.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-282  924.5   0.1   1.6e-282  924.3   0.1    1.0  1  NCBI__GCF_000746075.1:WP_048080955.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000746075.1:WP_048080955.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  924.3   0.1  1.6e-282  1.6e-282       3     627 ..      35     647 ..      33     649 .. 0.98

  Alignments for each domain:
  == domain 1  score: 924.3 bits;  conditional E-value: 1.6e-282
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkv 74 
                                           ++++y el ++a+++p+ fw++lake lew++p+++vl+++ +p+++Wf +g+ n++ n++drh+++ + dk+
  NCBI__GCF_000746075.1:WP_048080955.1  35 KIKNYDELLKKANDNPDWFWDDLAKE-LEWFEPYKNVLKWD-PPHAEWFLEGKFNIAHNALDRHIKNgKGDKI 105
                                           6799*********************5.*************9.88***********************9***** PP

                             TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147
                                           a iweg++ +  +rk+tY++l  +v+++an+l+elG+ kgd+v+iYlpmipe+ +amlaca+iGavhsvvf+G
  NCBI__GCF_000746075.1:WP_048080955.1 106 AYIWEGEDGK--TRKITYHQLWCDVNKFANALRELGIGKGDTVSIYLPMIPELPVAMLACAKIGAVHSVVFSG 176
                                           *******775..6************************************************************ PP

                             TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220
                                           f a+a++eR++d+++k+ it+d+ +R+gk i+lk++vd+ l++++ ++++ +v++ +g +v+ ++egrD+ww+
  NCBI__GCF_000746075.1:WP_048080955.1 177 FWAKAFQERVNDSKSKVAITTDGFTRRGKLIPLKENVDDILQNTP-TIKNLIVINNAGIDVK-MHEGRDLWWH 247
                                           ********************************************9.7*************76.********** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           e++e + s+ece+e +dsedplfiLYtsG+tGkPkGv+h  gGy++ +++t k+vfd++++di+wC+aD+GW+
  NCBI__GCF_000746075.1:WP_048080955.1 248 EITE-NMSEECETEVMDSEDPLFILYTSGTTGKPKGVVHVHGGYAVGIYTTLKFVFDLNEDDIWWCAADIGWI 319
                                           ****.5******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGhsYivy+PL+ G+t+++feg+p+ypd++r+w+++e ykv++fYtaPt iR++mk+g ++++k+dlss+r+l
  NCBI__GCF_000746075.1:WP_048080955.1 320 TGHSYIVYAPLLLGVTSIIFEGTPDYPDPGRLWKIVEGYKVNVFYTAPTTIRMFMKYGPKWPQKYDLSSIRLL 392
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           gsvGepinpeaw Wyy+++G+ekcpi+dtwWqtetG +litplp    +lkpgsa +P++ ++a+++d+ g++
  NCBI__GCF_000746075.1:WP_048080955.1 393 GSVGEPINPEAWVWYYKYIGREKCPIMDTWWQTETGMHLITPLPI--SPLKPGSAVMPFPTVQADILDDMGRS 463
                                           ********************************************8..6************************* PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512
                                           ++e+  gg Lvik+pwPsmlrtiy++++r+++tY++++k++y++GD ar+d+dGy+wi+GR Ddv+ v+Ghr+
  NCBI__GCF_000746075.1:WP_048080955.1 464 LTEK--GGHLVIKTPWPSMLRTIYRNPQRYIKTYWSAFKNMYLSGDVARKDSDGYFWIQGREDDVLSVAGHRI 534
                                           9874..468**************************************************************** PP

                             TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585
                                           gtae+esalvs e vaeaavvg+pdeikge i+afv+lk++ ++++e l+++lk +vr eigp+a+p+ i +v
  NCBI__GCF_000746075.1:WP_048080955.1 535 GTAEVESALVSYECVAEAAVVGKPDEIKGEEIAAFVILKDNFKPTQE-LKDTLKYHVRVEIGPVATPKYISFV 606
                                           *********************************************95.************************* PP

                             TIGR02188 586 eelPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627
                                           ++lPktRsGkimRR++++ ++ge++ gd+stl++p++v+ l 
  NCBI__GCF_000746075.1:WP_048080955.1 607 DDLPKTRSGKIMRRVIKAKVKGEDV-GDTSTLANPEAVDGLD 647
                                           ******************9998876.5**********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (650 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: 30.23
//
[ok]

This GapMind analysis is from Sep 24 2021. 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