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_048082644.1 EI99_RS14430 acetate--CoA ligase

Query= BRENDA::Q2XNL6
         (634 letters)



>NCBI__GCF_000746075.1:WP_048082644.1
          Length = 634

 Score = 1056 bits (2731), Expect = 0.0
 Identities = 482/634 (76%), Positives = 567/634 (89%)

Query: 1   MSKDTSVLLEEKRVFKPHYTVVEEAHIKNWEAELEKGKDHENYWAEKAERLEWFRKWDRV 60
           M  DT VLL E+RVFKP   +++  H+K+WE+E+EKGKD E YWAEKAE+  WF+KWD+V
Sbjct: 1   MRHDTDVLLNEERVFKPGQEIIDVLHVKDWESEIEKGKDIEKYWAEKAEQFVWFKKWDKV 60

Query: 61  LDESNRPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVS 120
           LD+SN PFY+WFVNGKINM YNAVDRW+ TDKRNQVA+LYVNERG E+KLTYYELYREV+
Sbjct: 61  LDDSNEPFYKWFVNGKINMAYNAVDRWITTDKRNQVAVLYVNERGHEKKLTYYELYREVN 120

Query: 121 RTANALKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDA 180
           + ANALK+LG+KKGD V+ YLPMCPEL+V +LAC KIGA+HSV+YSGLSVGA VER+ND 
Sbjct: 121 KFANALKNLGVKKGDVVSTYLPMCPELMVVLLACTKIGAIHSVVYSGLSVGAFVERINDC 180

Query: 181 RAKIIITADGTYRRGGVIKLKPIVDEAILQCPTIETTVVVKHTDIDIEMSDISGREMLFD 240
            AKI+ITADGT+RRG +I LK + DEA+LQCPT+ET VVVKHT I IEMS++SGRE+ ++
Sbjct: 181 NAKILITADGTFRRGKIIDLKRVSDEAMLQCPTVETVVVVKHTGIPIEMSELSGREIFYE 240

Query: 241 KLIEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHNG 300
            LIEGE    +AEEMDAEDPLFILYTSGSTGKPKGVLHTT GYMVGVA+TL   F+IH+G
Sbjct: 241 TLIEGEPAELEAEEMDAEDPLFILYTSGSTGKPKGVLHTTAGYMVGVATTLNNVFNIHDG 300

Query: 301 DLWWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTAP 360
           DLWWCT DIGWITGHS+++YGPLLLGTTTL+YEGAPDYP+PG WWS+VEKYGVTK YTAP
Sbjct: 301 DLWWCTGDIGWITGHSFLLYGPLLLGTTTLVYEGAPDYPNPGAWWSVVEKYGVTKLYTAP 360

Query: 361 TAIRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTET 420
           TAIRHLMRFG K+P  YNL SLKILGTVGEPINPEAWMW+Y+N+G+EKCPI+DTWWQTET
Sbjct: 361 TAIRHLMRFGSKYPNLYNLSSLKILGTVGEPINPEAWMWFYKNVGKEKCPIMDTWWQTET 420

Query: 421 GMHLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLFN 480
           GMH+I+PLP+ PLKPGS T  LPGI+ADVVD+ G+PVP+GKGG LVI+KPWPAMFRTL+N
Sbjct: 421 GMHMISPLPIAPLKPGSATMALPGIDADVVDDEGNPVPVGKGGLLVIKKPWPAMFRTLYN 480

Query: 481 DEQRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFVA 540
           DE+++I+ YWK++PG VYTAGD+ARKDEDGYFWIQGRSDDVL IAGHRIGT+EVES FV+
Sbjct: 481 DEEKFINTYWKEVPGCVYTAGDIARKDEDGYFWIQGRSDDVLKIAGHRIGTSEVESAFVS 540

Query: 541 HPAVAEAAVIGKADPIKGEVIKAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMVQ 600
           HPAV EAAVIGK+DPIKGEVIKAF+ILK+G++L   LIE+L RH+R+ELGPVAV+G++ Q
Sbjct: 541 HPAVVEAAVIGKSDPIKGEVIKAFVILKEGYQLKTQLIEDLSRHVRYELGPVAVLGQITQ 600

Query: 601 VDSLPKTRSGKIMRRILRAREEGEDLGDTSTLEE 634
           VDSLPKTRSGKIMRR+LRAR+ GED+GD STLEE
Sbjct: 601 VDSLPKTRSGKIMRRVLRARDRGEDVGDISTLEE 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: 1470
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_048082644.1 EI99_RS14430 (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.3506959.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.4e-268  876.3   0.2   6.5e-268  876.0   0.2    1.0  1  NCBI__GCF_000746075.1:WP_048082644.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000746075.1:WP_048082644.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  876.0   0.2  6.5e-268  6.5e-268      14     619 ..      36     634 .]      25     634 .] 0.97

  Alignments for each domain:
  == domain 1  score: 876.0 bits;  conditional E-value: 6.5e-268
                             TIGR02188  14 aiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaiiwegdeege 85 
                                             +d+ek+wa++a+ ++ w+k+++kvld+s+ep++kWf++g++n++yn+vdr++++ ++++va+ +  +  + 
  NCBI__GCF_000746075.1:WP_048082644.1  36 KGKDIEKYWAEKAE-QFVWFKKWDKVLDDSNEPFYKWFVNGKINMAYNAVDRWITTdKRNQVAVLYVNERGH- 106
                                           4589*********9.5***************************************9999*******999544. PP

                             TIGR02188  86 dsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRiv 158
                                            ++kltY+el+rev+++an+lk+lGvkkgd v+ Ylpm pe+++++lac++iGa+hsvv++G s  a+ eRi+
  NCBI__GCF_000746075.1:WP_048082644.1 107 -EKKLTYYELYREVNKFANALKNLGVKKGDVVSTYLPMCPELMVVLLACTKIGAIHSVVYSGLSVGAFVERIN 178
                                           .7*********************************************************************** PP

                             TIGR02188 159 daeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewke..grDvwweelvekeasa 229
                                           d++ak++itad+++R+gk+i+lk++ dea+ +++ +ve+v+vvk+tg +++ ++e  gr++ +e+l+e +++a
  NCBI__GCF_000746075.1:WP_048082644.1 179 DCNAKILITADGTFRRGKIIDLKRVSDEAMLQCP-TVETVVVVKHTGIPIE-MSElsGREIFYETLIE-GEPA 248
                                           *********************************9.7*************76.654449**********.6*** PP

                             TIGR02188 230 ecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivyg 302
                                           e+e+e++d+edplfiLYtsGstGkPkGvlhtt+Gy++ +a+t + vf+i+d+d +wCt+D+GW+tGhs+++yg
  NCBI__GCF_000746075.1:WP_048082644.1 249 ELEAEEMDAEDPLFILYTSGSTGKPKGVLHTTAGYMVGVATTLNNVFNIHDGDLWWCTGDIGWITGHSFLLYG 321
                                           ************************************************************************* PP

                             TIGR02188 303 PLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinp 375
                                           PL+ G ttl++eg+p+yp+++ +w+v+eky+vt++YtaPtaiR lm+ g++ ++ ++lssl++lg+vGepinp
  NCBI__GCF_000746075.1:WP_048082644.1 322 PLLLGTTTLVYEGAPDYPNPGAWWSVVEKYGVTKLYTAPTAIRHLMRFGSKYPNLYNLSSLKILGTVGEPINP 394
                                           ************************************************************************* PP

                             TIGR02188 376 eaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggv 448
                                           eaw+W+y++vGkekcpi+dtwWqtetG ++i+plp   ++lkpgsat+ l+Gi+a+vvd+eg++v  +++ g+
  NCBI__GCF_000746075.1:WP_048082644.1 395 EAWMWFYKNVGKEKCPIMDTWWQTETGMHMISPLPI--APLKPGSATMALPGIDADVVDDEGNPVPVGKG-GL 464
                                           ***********************************8..6****************************999.8* PP

                             TIGR02188 449 LvikkpwPsmlrtiygdeerfvetYfkklkg.lyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesa 520
                                           LvikkpwP+m+rt+y+dee+f++tY+k+++g +y +GD ar+d+dGy+wi+GR Ddv++++Ghr+gt+e+esa
  NCBI__GCF_000746075.1:WP_048082644.1 465 LVIKKPWPAMFRTLYNDEEKFINTYWKEVPGcVYTAGDIARKDEDGYFWIQGRSDDVLKIAGHRIGTSEVESA 537
                                           ******************************98999************************************** PP

                             TIGR02188 521 lvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRs 593
                                           +vsh+av eaav+g++d ikge+i afv+lkeg++ ++ +l ++l ++vr e+gp+a   +i+ v++lPktRs
  NCBI__GCF_000746075.1:WP_048082644.1 538 FVSHPAVVEAAVIGKSDPIKGEVIKAFVILKEGYQLKT-QLIEDLSRHVRYELGPVAVLGQITQVDSLPKTRS 609
                                           ***********************************999.6********************************* PP

                             TIGR02188 594 GkimRRllrkiaegeellgdvstled 619
                                           GkimRR+lr+  +ge  +gd+stle+
  NCBI__GCF_000746075.1:WP_048082644.1 610 GKIMRRVLRARDRGE-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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 22.00
//
[ok]

This GapMind analysis is from Sep 24 2021. 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)
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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