Alignments for a candidate for acs in Oceanisphaera arctica V1-41

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Oceanisphaera arctica V1-41

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_104486250.1 UN63_RS07990 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_002936955.1:WP_104486250.1
          Length = 649

 Score = 1023 bits (2646), Expect = 0.0
 Identities = 475/649 (73%), Positives = 552/649 (85%)

Query: 1   MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60
           MS++  H + A  A+  LI+   Y+ MYQ+SI  PD FWGEQGK +DWIKPY KVKNTS+
Sbjct: 1   MSEVKVHPVMAQFAEHALIDDAGYQRMYQESIENPDKFWGEQGKQVDWIKPYTKVKNTSY 60

Query: 61  APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120
            PG++SIKW+EDGTLNL+ANC+DRHL    D  AIIWEGD     K ++Y+ELH  VCRF
Sbjct: 61  DPGHISIKWFEDGTLNLSANCIDRHLATKADEVAIIWEGDSPDDDKKVTYRELHEQVCRF 120

Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180
           AN L   G+KKGDVV+IYMPMV EAAVAMLACARIGAVHSV+FGGFSP+A+A R+IDS +
Sbjct: 121 ANVLKAQGVKKGDVVSIYMPMVVEAAVAMLACARIGAVHSVVFGGFSPDALASRVIDSEA 180

Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240
           +LVIT+DEG+R GR++ LK NVD AL  P V+    V+V +RTGG + W E RD+WWH+ 
Sbjct: 181 KLVITADEGLRGGRTVALKANVDAALAKPGVSQDCKVIVYRRTGGDVAWFENRDIWWHEA 240

Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300
             + S +    EMNAEDPLFILYTSGSTG PKGVLHTTGGYLVYAA+TFKY+FDYH GD+
Sbjct: 241 TAKVSAECPPTEMNAEDPLFILYTSGSTGTPKGVLHTTGGYLVYAAMTFKYIFDYHEGDV 300

Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360
           +WCTADVGWVTGH+Y+LYGPLA GATTLMFEGVPN+P   RMAQ+VDKHQVNILYTAPTA
Sbjct: 301 HWCTADVGWVTGHTYILYGPLANGATTLMFEGVPNYPKTNRMAQIVDKHQVNILYTAPTA 360

Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420
           IRA MA+GD+A+EGT R+SLR+LGSVGEPINPEAWEWY++ IG+E+CP+VDTWWQTETGG
Sbjct: 361 IRAFMAKGDEAVEGTSRASLRVLGSVGEPINPEAWEWYYRVIGDERCPIVDTWWQTETGG 420

Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480
            +I PLPGAT LKAGSATRPFFGVQPALVD EG  L+G T+G+LVI DSWPGQ RT+FGD
Sbjct: 421 ILICPLPGATLLKAGSATRPFFGVQPALVDGEGTVLDGVTDGNLVILDSWPGQMRTIFGD 480

Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540
           H+RFEQTYFSTF   YFSGDGARRDEDGYYWITGRVDDVLNVSGHR+GTAEIESALVAHP
Sbjct: 481 HDRFEQTYFSTFPGTYFSGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESALVAHP 540

Query: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600
           KIAEAAVVG+PH+IKGQ IYAYVTLN GE PS EL+ EV++WVRKEIGP+ATPD++HW +
Sbjct: 541 KIAEAAVVGVPHDIKGQGIYAYVTLNSGEVPSAELHKEVKDWVRKEIGPIATPDIIHWAE 600

Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIA 649
            LPKTRSGKIMRRILRKIA GDT +LGDTSTLADP VV++L+EE+  +A
Sbjct: 601 GLPKTRSGKIMRRILRKIATGDTGSLGDTSTLADPAVVDRLIEERSRVA 649


Lambda     K      H
   0.317    0.135    0.421 

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: 1566
Number of extensions: 64
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: 652
Length of database: 649
Length adjustment: 38
Effective length of query: 614
Effective length of database: 611
Effective search space:   375154
Effective search space used:   375154
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_104486250.1 UN63_RS07990 (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.1648799.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
          0 1021.5   0.2          0 1021.3   0.2    1.0  1  NCBI__GCF_002936955.1:WP_104486250.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002936955.1:WP_104486250.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1021.3   0.2         0         0       6     628 ..      23     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1021.3 bits;  conditional E-value: 0
                             TIGR02188   6 eykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkva 75 
                                            y+++y+e+ie+p+kfw++++k +++w+kp++kv+++s +p   ++kWfedg+ln+s+nc+drh+++++d+va
  NCBI__GCF_002936955.1:WP_104486250.1  23 GYQRMYQESIENPDKFWGEQGK-QVDWIKPYTKVKNTSYDPghiSIKWFEDGTLNLSANCIDRHLATKADEVA 94 
                                           69********************.5***************999899**************************** PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           iiwegd+++ d +k+tY+el+++vcr+anvlk++Gvkkgd v+iY+pm++ea++amlacaRiGavhsvvf+Gf
  NCBI__GCF_002936955.1:WP_104486250.1  95 IIWEGDSPD-DDKKVTYRELHEQVCRFANVLKAQGVKKGDVVSIYMPMVVEAAVAMLACARIGAVHSVVFGGF 166
                                           ******998.59************************************************************* PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwwe 220
                                           s++ala+R++d+eaklvitadeglRgg++++lk++vd+al+k    +  kv+v++rtg +va w e+rD+ww+
  NCBI__GCF_002936955.1:WP_104486250.1 167 SPDALASRVIDSEAKLVITADEGLRGGRTVALKANVDAALAKPGVsQDCKVIVYRRTGGDVA-WFENRDIWWH 238
                                           ******************************************98866679**********77.********** PP

                             TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293
                                           e+++k +saec+p+++++edplfiLYtsGstG+PkGvlhttgGyl++aa+t+ky+fd++++d++wCtaDvGWv
  NCBI__GCF_002936955.1:WP_104486250.1 239 EATAK-VSAECPPTEMNAEDPLFILYTSGSTGTPKGVLHTTGGYLVYAAMTFKYIFDYHEGDVHWCTADVGWV 310
                                           ****7.******************************************************************* PP

                             TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366
                                           tGh+Yi+ygPLanGattl+fegvp+yp+++r++++++k++v+i+YtaPtaiRa+m++g+e+v+ +++ slrvl
  NCBI__GCF_002936955.1:WP_104486250.1 311 TGHTYILYGPLANGATTLMFEGVPNYPKTNRMAQIVDKHQVNILYTAPTAIRAFMAKGDEAVEGTSRASLRVL 383
                                           ************************************************************************* PP

                             TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                           gsvGepinpeaweWyy+v+G+e+cpivdtwWqtetGgili plpg at lk+gsat+P+fG+++++vd eg+ 
  NCBI__GCF_002936955.1:WP_104486250.1 384 GSVGEPINPEAWEWYYRVIGDERCPIVDTWWQTETGGILICPLPG-ATLLKAGSATRPFFGVQPALVDGEGTV 455
                                           *********************************************.6************************** PP

                             TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512
                                           ++  ++ g Lvi ++wP+++rti+gd++rf +tYf++++g+yf+GDgarrd+dGy+wi+GRvDdv+nvsGhr+
  NCBI__GCF_002936955.1:WP_104486250.1 456 LDGVTD-GNLVILDSWPGQMRTIFGDHDRFEQTYFSTFPGTYFSGDGARRDEDGYYWITGRVDDVLNVSGHRM 527
                                           *97777.89**************************************************************** PP

                             TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585
                                           gtaeiesalv+h+++aeaavvgvp++ikg+ i+a+v+l++g+ +++e l+ke+k++vrkeigpia+pd i+++
  NCBI__GCF_002936955.1:WP_104486250.1 528 GTAEIESALVAHPKIAEAAVVGVPHDIKGQGIYAYVTLNSGEVPSAE-LHKEVKDWVRKEIGPIATPDIIHWA 599
                                           *********************************************95.************************* PP

                             TIGR02188 586 eelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           e lPktRsGkimRR+lrkia+g+  +lgd+stl+dp+vv++l+e
  NCBI__GCF_002936955.1:WP_104486250.1 600 EGLPKTRSGKIMRRILRKIATGDtGSLGDTSTLADPAVVDRLIE 643
                                           ***********************999**************9987 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 31.73
//
[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