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_013645469.1 METBO_RS09375 acetate--CoA ligase

Query= BRENDA::Q2XNL6
         (634 letters)



>NCBI__GCF_000191585.1:WP_013645469.1
          Length = 633

 Score = 1061 bits (2745), Expect = 0.0
 Identities = 488/634 (76%), Positives = 567/634 (89%), Gaps = 1/634 (0%)

Query: 1   MSKDTSVLLEEKRVFKPHYTVVEEAHIKNWEAELEKGKDHENYWAEKAERLEWFRKWDRV 60
           M +DT+VLL+EKR+FKP    VE AH+KNWE E+EKGK+ E YW EKAE LEWF KWD+V
Sbjct: 1   MKRDTTVLLDEKRIFKPDVETVERAHVKNWENEIEKGKNFEAYWEEKAEELEWFEKWDKV 60

Query: 61  LDESNRPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVS 120
           LDE+N+PFY+W+VNGKIN+TYNAVDRW+ T+KRNQVAILY+NERGDE KLTYYELYR+V+
Sbjct: 61  LDETNKPFYQWYVNGKINLTYNAVDRWIYTEKRNQVAILYINERGDEEKLTYYELYRQVN 120

Query: 121 RTANALKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDA 180
           + AN LK+LG+ KGD V++YLPMCPEL++SMLACAKIGAVHSV+YSGLSVGA VER+NDA
Sbjct: 121 KMANGLKNLGVNKGDTVSMYLPMCPELLISMLACAKIGAVHSVVYSGLSVGAFVERMNDA 180

Query: 181 RAKIIITADGTYRRGGVIKLKPIVDEAILQCPTIETTVVVKHTDIDIEMSDISGREMLFD 240
            AKI+ITADGTYRRG +I LK I DEA+LQCPTIET +V+KHT  +I +SD+SGRE+ +D
Sbjct: 181 NAKILITADGTYRRGKIINLKKISDEALLQCPTIETVIVLKHTGSEINVSDLSGREIFYD 240

Query: 241 KLIEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHNG 300
           + +EGE   C+ E MDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVA+TL+  FDI   
Sbjct: 241 RFLEGEPAECEPEWMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVATTLKNIFDIQKD 300

Query: 301 DLWWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTAP 360
           DLWWCT DIGWITGHSYV+YGPLLLGTTT++YEGAPDYPDPG WW I+EK+GVTKFYTAP
Sbjct: 301 DLWWCTGDIGWITGHSYVIYGPLLLGTTTIVYEGAPDYPDPGAWWKIIEKHGVTKFYTAP 360

Query: 361 TAIRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTET 420
           TAIRHLMRFG+K+P  YNL SL+ILGTVGEPINPEAWMW+Y+N+G+EK PI+DTWWQTET
Sbjct: 361 TAIRHLMRFGNKYPNIYNLSSLRILGTVGEPINPEAWMWFYKNVGKEKTPIMDTWWQTET 420

Query: 421 GMHLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLFN 480
           GMHLI+PLP   LKPGS TKP PG++ADVVDE+G+PVPLGKGG+LVI+KPWPAMFRTL+ 
Sbjct: 421 GMHLISPLPSAHLKPGSATKPFPGVDADVVDEDGNPVPLGKGGYLVIKKPWPAMFRTLYE 480

Query: 481 DEQRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFVA 540
           DE+R+  VYW QIP GVY AGDMARKDEDGYFWIQGRSDDVL IAGHR+GTAEVES FV+
Sbjct: 481 DEERFQQVYWNQIP-GVYKAGDMARKDEDGYFWIQGRSDDVLKIAGHRVGTAEVESAFVS 539

Query: 541 HPAVAEAAVIGKADPIKGEVIKAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMVQ 600
           HPAVAEAAVIGK+DPIKG+VIKAFLILK+G++L   LIEEL +H+R+ELGPVAV+GEM Q
Sbjct: 540 HPAVAEAAVIGKSDPIKGQVIKAFLILKEGYQLKTKLIEELNKHVRYELGPVAVIGEMEQ 599

Query: 601 VDSLPKTRSGKIMRRILRAREEGEDLGDTSTLEE 634
           V+ LPKTRSGKIMRR+LRA+E GEDLGDTSTLEE
Sbjct: 600 VEKLPKTRSGKIMRRLLRAKESGEDLGDTSTLEE 633


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: 1527
Number of extensions: 69
Number of successful extensions: 2
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: 633
Length adjustment: 38
Effective length of query: 596
Effective length of database: 595
Effective search space:   354620
Effective search space used:   354620
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_013645469.1 METBO_RS09375 (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.1839536.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.9e-274  896.3   0.1     6e-274  896.0   0.1    1.0  1  NCBI__GCF_000191585.1:WP_013645469.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000191585.1:WP_013645469.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  896.0   0.1    6e-274    6e-274      14     619 ..      36     633 .]      24     633 .] 0.97

  Alignments for each domain:
  == domain 1  score: 896.0 bits;  conditional E-value: 6e-274
                             TIGR02188  14 aiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaiiwegdeege 85 
                                             ++ e++w+++a+ elew+++++kvlde+++p+++W+++g++n++yn+vdr++ + ++++vai +  + +g 
  NCBI__GCF_000191585.1:WP_013645469.1  36 KGKNFEAYWEEKAE-ELEWFEKWDKVLDETNKPFYQWYVNGKINLTYNAVDRWIYTeKRNQVAILYINE-RG- 105
                                           45789********9.5**************************************99899*******999.55. PP

                             TIGR02188  86 dsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRiv 158
                                           d++kltY+el+r+v+++an lk+lGv+kgd+v++Ylpm pe+ i mlaca+iGavhsvv++G s  a+ eR++
  NCBI__GCF_000191585.1:WP_013645469.1 106 DEEKLTYYELYRQVNKMANGLKNLGVNKGDTVSMYLPMCPELLISMLACAKIGAVHSVVYSGLSVGAFVERMN 178
                                           489********************************************************************** PP

                             TIGR02188 159 daeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaew.kegrDvwweelvekeasae 230
                                           da+ak++itad+++R+gk+i+lkki deal +++ ++e+v+v+k+tg+e++    +gr++ +++ +e +++ae
  NCBI__GCF_000191585.1:WP_013645469.1 179 DANAKILITADGTYRRGKIINLKKISDEALLQCP-TIETVIVLKHTGSEINVSdLSGREIFYDRFLE-GEPAE 249
                                           *********************************9.7*************87331469**********.6**** PP

                             TIGR02188 231 cepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygP 303
                                           cepe++d+edplfiLYtsGstGkPkGvlhttgGy++ +a+t k +fdi+++d +wCt+D+GW+tGhsY++ygP
  NCBI__GCF_000191585.1:WP_013645469.1 250 CEPEWMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVATTLKNIFDIQKDDLWWCTGDIGWITGHSYVIYGP 322
                                           ************************************************************************* PP

                             TIGR02188 304 LanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpe 376
                                           L+ G tt+++eg+p+ypd++ +w++iek++vt+fYtaPtaiR lm+ g++ ++ ++lsslr+lg+vGepinpe
  NCBI__GCF_000191585.1:WP_013645469.1 323 LLLGTTTIVYEGAPDYPDPGAWWKIIEKHGVTKFYTAPTAIRHLMRFGNKYPNIYNLSSLRILGTVGEPINPE 395
                                           ************************************************************************* PP

                             TIGR02188 377 aweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvL 449
                                           aw+W+y++vGkek+pi+dtwWqtetG +li+plp+  ++lkpgsat+P++G++a+vvde+g++v  +++ g+L
  NCBI__GCF_000191585.1:WP_013645469.1 396 AWMWFYKNVGKEKTPIMDTWWQTETGMHLISPLPS--AHLKPGSATKPFPGVDADVVDEDGNPVPLGKG-GYL 465
                                           ***********************************..5****************************999.8** PP

                             TIGR02188 450 vikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalv 522
                                           vikkpwP+m+rt+y+deerf+++Y+++++g+y +GD+ar+d+dGy+wi+GR Ddv++++Ghr+gtae+esa+v
  NCBI__GCF_000191585.1:WP_013645469.1 466 VIKKPWPAMFRTLYEDEERFQQVYWNQIPGVYKAGDMARKDEDGYFWIQGRSDDVLKIAGHRVGTAEVESAFV 538
                                           ************************************************************************* PP

                             TIGR02188 523 sheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGk 595
                                           sh+avaeaav+g++d ikg++i af++lkeg++ ++ +l +el+k+vr e+gp+a   +++ ve+lPktRsGk
  NCBI__GCF_000191585.1:WP_013645469.1 539 SHPAVAEAAVIGKSDPIKGQVIKAFLILKEGYQLKT-KLIEELNKHVRYELGPVAVIGEMEQVEKLPKTRSGK 610
                                           *********************************999.5*********************************** PP

                             TIGR02188 596 imRRllrkiaegeellgdvstled 619
                                           imRRllr+  +g e lgd+stle+
  NCBI__GCF_000191585.1:WP_013645469.1 611 IMRRLLRAKESG-EDLGDTSTLEE 633
                                           *******86665.5677*****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (633 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: 20.72
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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