Alignments for a candidate for acs in Methanobacterium lacus AL-21

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Methanobacterium lacus AL-21

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_013644169.1 METBO_RS02895 acetate--CoA ligase

Query= BRENDA::A0B8F1
         (659 letters)



>NCBI__GCF_000191585.1:WP_013644169.1
          Length = 649

 Score =  763 bits (1970), Expect = 0.0
 Identities = 360/646 (55%), Positives = 467/646 (72%), Gaps = 8/646 (1%)

Query: 10  LQEETRIFNTPQWIIEYSNSYQWMKKKGFKTEKEMREWCAQNYLDFWDEMAQTYADWFKP 69
           L +E RIF      ++ SN Y+WM+K+  K   E+ E   ++   FWDE+A    +WF+P
Sbjct: 8   LLKEKRIFKPSLEFVKDSNIYKWMEKRNIKDYDELLELAEKDPEWFWDELAHEL-EWFEP 66

Query: 70  YTQILEWNPPYAKWFLGGKCNVAHNAVDRHAKSWRRNKVAYYFVGEPVGDTKTITYYQLY 129
           YT+   WNPP+A+WF+ GK N+  NA+DRHA   +++K A+ + GE  G+ +++TY QL 
Sbjct: 67  YTKTFNWNPPHAEWFVNGKFNIVQNAIDRHAHGEQKDKTAFIWEGES-GEVRSLTYKQLQ 125

Query: 130 QAVNKMANGLKSLGVKKGDRVSIYLPMIPELPITMLACAKIGAIHSVVFSGFSAGGLQSR 189
             VNK AN L+ LGVKKGD VSIYLPMI ELPI MLACAKIGAIHSVVFSGF A   Q R
Sbjct: 126 MQVNKFANVLRDLGVKKGDTVSIYLPMILELPIAMLACAKIGAIHSVVFSGFWAKAFQER 185

Query: 190 VTDAEAKVVVTSDGFYRRGKPLPLKPNVDEAVQNAPSVEKVVVVKRVGLDVPMKEGRDIW 249
           + DA++KV +T+DGF RRGK + LK NVD  ++N PS++K++VV+   + + M   RDIW
Sbjct: 186 INDADSKVAITADGFTRRGKQICLKENVDVILENTPSIQKLIVVEHAKIPIEMDSNRDIW 245

Query: 250 YHDLVKDQPAECYTEELDPEDRLFILYTSGTTGKPKGIEHAHGGFCVGPAYTTAWALDVH 309
           +H+ ++    EC TEE+DPED LFILYTSGTTGKPKG+ H HGG+ VG   T  +  D+ 
Sbjct: 246 WHEAMEKAVFECTTEEMDPEDPLFILYTSGTTGKPKGVVHVHGGYGVGVYTTLKFVFDIK 305

Query: 310 EEDVYWCTADCGWITGHSYVVYGPLCLGATSILYEGAPDYPDIGRWWSIIEEYGVSVFYT 369
            +D++WC AD GWITGHSY+VY PL +GATS++YEG PDYPD GR WS+IE+Y VSVFYT
Sbjct: 306 PDDIWWCAADIGWITGHSYIVYAPLMMGATSVIYEGTPDYPDPGRVWSMIEKYNVSVFYT 365

Query: 370 APTAIRMFMKAGDQWPKKYNLKSIRILASVGEPLNPEAYVWFRNNIGGGQAPIIDTWWQT 429
           APT +RMFMK G++WP+KY++ S+R+L SVGEP+NPEA++W+   IG  + PI+DTWWQT
Sbjct: 366 APTTVRMFMKFGEKWPEKYDISSLRLLGSVGEPINPEAWIWYHEVIGKSRCPIMDTWWQT 425

Query: 430 ETGCHVIAPLPMTPEKPGSVAFPLPGFNTDIYDEDGNSVPLGYGGNIVQKTPWPSMLRAF 489
           ETG H+I PLP++  KPGS   P P    D+ D+DGNS+  G GG++V K+ WP+M R  
Sbjct: 426 ETGMHLITPLPISDLKPGSAVKPFPTIVADVIDDDGNSIK-GGGGHLVIKSTWPAMFRTL 484

Query: 490 FRDPERYMKEYWQMYWDIKPGTYLAGDKATRDKDGYWWIQGRIDDVLKVAGHRISNAEVE 549
           + DP RY     + YW     TYL+GD A +D DGY+WIQGR DDVL VAGHRIS AEVE
Sbjct: 485 YNDPNRY-----EAYWSSFKNTYLSGDVARKDDDGYFWIQGREDDVLNVAGHRISTAEVE 539

Query: 550 SAAVSHPAVAEAAVIGKPDEVKGEVIVAFIILKEGVQESEDLKKDIAKHVRSVLGPVAYP 609
           SA VSHP VAEAAV+GKPDE+KGE I AF+++KE        +  +  HVR+ +GP+A P
Sbjct: 540 SALVSHPGVAEAAVVGKPDEIKGEEISAFVVIKENYHFETSYETVLRHHVRTEIGPIATP 599

Query: 610 EIVYFVKDVPKTRSGKIMRRVIKAKALGKPVGDISALANPESVENI 655
           + +  V D+PKTRSGKIMRRVIKA+  G+ VGD S LANPE+V+ I
Sbjct: 600 KYIKLVGDLPKTRSGKIMRRVIKARVKGETVGDTSTLANPEAVKEI 645


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: 1416
Number of extensions: 67
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: 649
Length adjustment: 38
Effective length of query: 621
Effective length of database: 611
Effective search space:   379431
Effective search space used:   379431
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_013644169.1 METBO_RS02895 (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.32434.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-279  913.3   1.2     4e-279  913.1   1.2    1.0  1  lcl|NCBI__GCF_000191585.1:WP_013644169.1  METBO_RS02895 acetate--CoA ligas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000191585.1:WP_013644169.1  METBO_RS02895 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  913.1   1.2    4e-279    4e-279       3     628 ..      35     647 ..      33     648 .. 0.98

  Alignments for each domain:
  == domain 1  score: 913.1 bits;  conditional E-value: 4e-279
                                 TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.r 70 
                                               ++++y el e a++dpe fw++la+e lew++p++k+++++ +p+++Wf++g+ n+  n++drh++  +
  lcl|NCBI__GCF_000191585.1:WP_013644169.1  35 NIKDYDELLELAEKDPEWFWDELAHE-LEWFEPYTKTFNWN-PPHAEWFVNGKFNIVQNAIDRHAHGeQ 101
                                               7899*********************5.*************9.88*********************988* PP

                                 TIGR02188  71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGa 139
                                               kdk+a iweg+ +g ++r+ltY++l+ +v+++anvl++lGvkkgd+v+iYlpmi e+ iamlaca+iGa
  lcl|NCBI__GCF_000191585.1:WP_013644169.1 102 KDKTAFIWEGE-SG-EVRSLTYKQLQMQVNKFANVLRDLGVKKGDTVSIYLPMILELPIAMLACAKIGA 168
                                               ***********.55.49**************************************************** PP

                                 TIGR02188 140 vhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeev 208
                                               +hsvvf+Gf a+a++eRi+da++k+ itad+ +R+gk+i lk++vd  le+++ s++k +vv++++ ++
  lcl|NCBI__GCF_000191585.1:WP_013644169.1 169 IHSVVFSGFWAKAFQERINDADSKVAITADGFTRRGKQICLKENVDVILENTP-SIQKLIVVEHAKIPI 236
                                               ****************************************************9.7*************6 PP

                                 TIGR02188 209 aewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfd 277
                                               + ++++rD+ww+e++ek a  ec++e++d edplfiLYtsG+tGkPkGv+h  gGy + +++t k+vfd
  lcl|NCBI__GCF_000191585.1:WP_013644169.1 237 E-MDSNRDIWWHEAMEK-AVFECTTEEMDPEDPLFILYTSGTTGKPKGVVHVHGGYGVGVYTTLKFVFD 303
                                               6.**************7.99************************************************* PP

                                 TIGR02188 278 ikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRa 346
                                               ik++di+wC+aD+GW+tGhsYivy+PL++Gat++++eg+p+ypd++r+w++ieky+v++fYtaPt +R+
  lcl|NCBI__GCF_000191585.1:WP_013644169.1 304 IKPDDIWWCAADIGWITGHSYIVYAPLMMGATSVIYEGTPDYPDPGRVWSMIEKYNVSVFYTAPTTVRM 372
                                               ********************************************************************* PP

                                 TIGR02188 347 lmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvate 415
                                               +mk ge++++k+d+sslr+lgsvGepinpeaw Wy+ev+Gk++cpi+dtwWqtetG +litplp    +
  lcl|NCBI__GCF_000191585.1:WP_013644169.1 373 FMKFGEKWPEKYDISSLRLLGSVGEPINPEAWIWYHEVIGKSRCPIMDTWWQTETGMHLITPLPI--SD 439
                                               ****************************************************************8..6* PP

                                 TIGR02188 416 lkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftG 484
                                               lkpgsa +P++ i a+v+d++g++++ +  gg Lvik++wP+m+rt+y+d++r+ e+Y++++k++y++G
  lcl|NCBI__GCF_000191585.1:WP_013644169.1 440 LKPGSAVKPFPTIVADVIDDDGNSIKGG--GGHLVIKSTWPAMFRTLYNDPNRY-EAYWSSFKNTYLSG 505
                                               ************************9874..468********************9.68************ PP

                                 TIGR02188 485 DgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkeg 553
                                               D ar+d+dGy+wi+GR Ddv+nv+Ghr++tae+esalvsh+ vaeaavvg+pdeikge i afvv+ke+
  lcl|NCBI__GCF_000191585.1:WP_013644169.1 506 DVARKDDDGYFWIQGREDDVLNVAGHRISTAEVESALVSHPGVAEAAVVGKPDEIKGEEISAFVVIKEN 574
                                               ********************************************************************* PP

                                 TIGR02188 554 veedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledpsv 622
                                               ++ ++ + e+ l+++vr+eigpia+p+ i++v +lPktRsGkimRR++++ ++ge+ +gd+stl++p++
  lcl|NCBI__GCF_000191585.1:WP_013644169.1 575 YHFET-SYETVLRHHVRTEIGPIATPKYIKLVGDLPKTRSGKIMRRVIKARVKGET-VGDTSTLANPEA 641
                                               ***99.5*******************************************999876.56********** PP

                                 TIGR02188 623 veelke 628
                                               v+e+++
  lcl|NCBI__GCF_000191585.1:WP_013644169.1 642 VKEIEK 647
                                               **9975 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 13.18
//
[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 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