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_013645290.1 METBO_RS08510 acetate--CoA ligase

Query= BRENDA::Q2XNL6
         (634 letters)



>NCBI__GCF_000191585.1:WP_013645290.1
          Length = 634

 Score = 1045 bits (2701), Expect = 0.0
 Identities = 484/634 (76%), Positives = 567/634 (89%)

Query: 1   MSKDTSVLLEEKRVFKPHYTVVEEAHIKNWEAELEKGKDHENYWAEKAERLEWFRKWDRV 60
           M +DT VLL+EKRVFKP   +++ A+IK+WEAE+EKGKD E YWAEKAE+  WF+K ++ 
Sbjct: 1   MKQDTDVLLDEKRVFKPSEEILKLANIKDWEAEIEKGKDIEKYWAEKAEQFVWFKKPEKT 60

Query: 61  LDESNRPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVS 120
           LDESN+PFY+WFVNGKINM YNAVDRW+DTDKRNQVAILYVNERG E+K+TYYELYREV+
Sbjct: 61  LDESNKPFYKWFVNGKINMAYNAVDRWIDTDKRNQVAILYVNERGHEKKMTYYELYREVN 120

Query: 121 RTANALKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDA 180
           + ANALK+LG+KKGD V+ YLPMC EL+V++LAC KIGAVHSV+YSGLSVGA VER+NDA
Sbjct: 121 KFANALKNLGVKKGDRVSTYLPMCTELIVTLLACTKIGAVHSVVYSGLSVGAFVERINDA 180

Query: 181 RAKIIITADGTYRRGGVIKLKPIVDEAILQCPTIETTVVVKHTDIDIEMSDISGREMLFD 240
            AKI+ITADGT+RRG +I LK + DEAILQCPTIET VVVKHT I IEMS++SGRE+ ++
Sbjct: 181 EAKILITADGTFRRGKIIDLKKVSDEAILQCPTIETVVVVKHTGIPIEMSELSGREIFYE 240

Query: 241 KLIEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHNG 300
            LIEGE   C+AEEMDAEDPLF+L+TSGSTGKPKGVLH+T GYMVG A+TL+  F+IH+G
Sbjct: 241 TLIEGEPAECEAEEMDAEDPLFLLFTSGSTGKPKGVLHSTAGYMVGTATTLKNAFNIHDG 300

Query: 301 DLWWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTAP 360
           DLWWCT DIGWITGHSY++YGPLLLGTTTL+YEGAPDYPDPG WW IVEKYGVTK YTAP
Sbjct: 301 DLWWCTGDIGWITGHSYLLYGPLLLGTTTLVYEGAPDYPDPGAWWKIVEKYGVTKLYTAP 360

Query: 361 TAIRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTET 420
           TAIRHLMRFG+K+ K YNL SLK+LGTVGEPINPEAWMW Y N+G+E CPIIDTWWQTET
Sbjct: 361 TAIRHLMRFGNKYTKIYNLSSLKVLGTVGEPINPEAWMWLYENVGKENCPIIDTWWQTET 420

Query: 421 GMHLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLFN 480
           GM +IAPLPVTPLKPGS TK LPG++ADVVDENG+ VP GKGG LVI+KPWP+MFRTL+ 
Sbjct: 421 GMFMIAPLPVTPLKPGSATKALPGVDADVVDENGNSVPPGKGGMLVIKKPWPSMFRTLYK 480

Query: 481 DEQRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFVA 540
           DE++Y+D YWK IPG VYTAGD+ARKD+DGYFWIQGRSDDVL IAGHRIGT+EVES FV+
Sbjct: 481 DEKKYVDNYWKDIPGCVYTAGDIARKDKDGYFWIQGRSDDVLKIAGHRIGTSEVESAFVS 540

Query: 541 HPAVAEAAVIGKADPIKGEVIKAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMVQ 600
           +PAV EAAVIGK+DPIKGEVIKAF+ILK+G++L   LIE+L +H+R+ELGPVAV+G++ Q
Sbjct: 541 YPAVVEAAVIGKSDPIKGEVIKAFVILKEGYELKTKLIEDLSKHVRYELGPVAVLGQIKQ 600

Query: 601 VDSLPKTRSGKIMRRILRAREEGEDLGDTSTLEE 634
           VDSLPKTRSGKI+RR+LRAR+ GED+GD STLEE
Sbjct: 601 VDSLPKTRSGKILRRVLRARDRGEDVGDISTLEE 634


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: 1444
Number of extensions: 63
Number of successful extensions: 1
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: 634
Length adjustment: 38
Effective length of query: 596
Effective length of database: 596
Effective search space:   355216
Effective search space used:   355216
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_013645290.1 METBO_RS08510 (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.21105.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-264  864.9   0.3   1.8e-264  864.6   0.3    1.0  1  lcl|NCBI__GCF_000191585.1:WP_013645290.1  METBO_RS08510 acetate--CoA ligas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000191585.1:WP_013645290.1  METBO_RS08510 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  864.6   0.3  1.8e-264  1.8e-264      13     619 ..      35     634 .]      24     634 .] 0.97

  Alignments for each domain:
  == domain 1  score: 864.6 bits;  conditional E-value: 1.8e-264
                                 TIGR02188  13 eaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaiiweg 80 
                                               e  +d+ek+wa++a+ ++ w+k+ ek+ldes++p++kWf++g++n++yn+vdr++ + ++++vai +  
  lcl|NCBI__GCF_000191585.1:WP_013645290.1  35 EKGKDIEKYWAEKAE-QFVWFKKPEKTLDESNKPFYKWFVNGKINMAYNAVDRWIDTdKRNQVAILYVN 102
                                               44589*********9.5***************************************9999*******99 PP

                                 TIGR02188  81 deegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfs 149
                                               +  +  ++k+tY+el+rev+++an+lk+lGvkkgdrv+ Ylpm +e+++++lac++iGavhsvv++G s
  lcl|NCBI__GCF_000191585.1:WP_013645290.1 103 ERGH--EKKMTYYELYREVNKFANALKNLGVKKGDRVSTYLPMCTELIVTLLACTKIGAVHSVVYSGLS 169
                                               9544..7************************************************************** PP

                                 TIGR02188 150 aealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewke..grD 216
                                                 a+ eRi+daeak++itad+++R+gk+i+lkk+ dea+ +++ ++e+v+vvk+tg +++ ++e  gr+
  lcl|NCBI__GCF_000191585.1:WP_013645290.1 170 VGAFVERINDAEAKILITADGTFRRGKIIDLKKVSDEAILQCP-TIETVVVVKHTGIPIE-MSElsGRE 236
                                               ******************************************9.7*************76.654449** PP

                                 TIGR02188 217 vwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifw 285
                                               + +e+l+e +++aece+e++d+edplf+L+tsGstGkPkGvlh+t+Gy++ +a+t k  f+i+d+d +w
  lcl|NCBI__GCF_000191585.1:WP_013645290.1 237 IFYETLIE-GEPAECEAEEMDAEDPLFLLFTSGSTGKPKGVLHSTAGYMVGTATTLKNAFNIHDGDLWW 304
                                               ********.6*********************************************************** PP

                                 TIGR02188 286 CtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeel 354
                                               Ct+D+GW+tGhsY++ygPL+ G ttl++eg+p+ypd++ +w+++eky+vt++YtaPtaiR lm+ g++ 
  lcl|NCBI__GCF_000191585.1:WP_013645290.1 305 CTGDIGWITGHSYLLYGPLLLGTTTLVYEGAPDYPDPGAWWKIVEKYGVTKLYTAPTAIRHLMRFGNKY 373
                                               ********************************************************************* PP

                                 TIGR02188 355 vkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatl 423
                                               +k ++lssl+vlg+vGepinpeaw+W+ye+vGke+cpi+dtwWqtetG ++i+plp   t+lkpgsat+
  lcl|NCBI__GCF_000191585.1:WP_013645290.1 374 TKIYNLSSLKVLGTVGEPINPEAWMWLYENVGKENCPIIDTWWQTETGMFMIAPLPV--TPLKPGSATK 440
                                               ********************************************************8..8********* PP

                                 TIGR02188 424 PlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg.lyftGDgarrdk 491
                                                l+G++a+vvde+g++v ++++ g+LvikkpwPsm+rt+y+de+++v+ Y+k+++g +y +GD ar+dk
  lcl|NCBI__GCF_000191585.1:WP_013645290.1 441 ALPGVDADVVDENGNSVPPGKG-GMLVIKKPWPSMFRTLYKDEKKYVDNYWKDIPGcVYTAGDIARKDK 508
                                               *******************999.8*******************************98999********* PP

                                 TIGR02188 492 dGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeee 560
                                               dGy+wi+GR Ddv++++Ghr+gt+e+esa+vs +av eaav+g++d ikge+i afv+lkeg+e ++ +
  lcl|NCBI__GCF_000191585.1:WP_013645290.1 509 DGYFWIQGRSDDVLKIAGHRIGTSEVESAFVSYPAVVEAAVIGKSDPIKGEVIKAFVILKEGYELKT-K 576
                                               *****************************************************************99.5 PP

                                 TIGR02188 561 lekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstled 619
                                               l ++l k+vr e+gp+a   +i+ v++lPktRsGki+RR+lr+  +ge  +gd+stle+
  lcl|NCBI__GCF_000191585.1:WP_013645290.1 577 LIEDLSKHVRYELGPVAVLGQIKQVDSLPKTRSGKILRRVLRARDRGE-DVGDISTLEE 634
                                               ******************************************877665.567*****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (634 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 11.82
//
[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