Alignments for a candidate for acs in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Echinicola vietnamensis KMM 6221, DSM 17526

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate Echvi_1268 Echvi_1268 acetate--CoA ligase

Query= reanno::pseudo5_N2C3_1:AO356_18695
         (651 letters)



>FitnessBrowser__Cola:Echvi_1268
          Length = 632

 Score =  721 bits (1861), Expect = 0.0
 Identities = 356/618 (57%), Positives = 441/618 (71%), Gaps = 6/618 (0%)

Query: 28  YQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVDIKWFADGTLNVSYNCLDRHLA 87
           YQ+SV  P+ FW   A    W K +  V +  F+    D+KWF +G +N++ N L+RHL 
Sbjct: 15  YQKSVTEPEQFWARIADSFHWKKRWDKVLEWDFEGP--DVKWFVNGKVNITENILERHLF 72

Query: 88  ERGDQIAIIWEGDDPSES-RNITYRELHEEVCKFANALRGQDVHRGDVVTIYMPMIPEAV 146
             GD+ AIIWE +DP+E  R +TYR+L+ EVCKF+NAL+ + + +GD V IYMPM+PEA 
Sbjct: 73  IMGDRPAIIWEPNDPNEEGRTLTYRQLYHEVCKFSNALKAKGIGKGDKVIIYMPMVPEAA 132

Query: 147 VAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITADEGVRAGKKIPLKANVDDAL 206
           +AMLAC RIGA+HSVVF GFS  ALA RI DC++K V+T+D   R  KKI +K  VD+AL
Sbjct: 133 IAMLACARIGAVHSVVFAGFSSSALADRINDCEAKAVLTSDGNFRGTKKIAVKDLVDEAL 192

Query: 207 TNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAGTVCAPKEMGAEEALFILYTSG 266
              +T +I+ VIV +RT   +K  + RDIW+ D +         + M +E+ LFILYTSG
Sbjct: 193 E--KTKTIETVIVYQRTKQEVKMVEGRDIWWHDAIDGQPDTNEAEVMDSEDMLFILYTSG 250

Query: 267 STGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTADVGWVTGHSYIVYGPLANGAT 326
           STGKPKGV HTT GY++Y+  T E VF Y PG+VYWCTAD+GW+TGHSYIVYGPL  GAT
Sbjct: 251 STGKPKGVVHTTGGYMVYSKYTFENVFQYSPGDVYWCTADIGWITGHSYIVYGPLLAGAT 310

Query: 327 TLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMMASGTAAVEGADGSSLRLLGSV 386
           +++FEGVP YPD  R   ++DK++V+  YTAPTAIRA+ A GT  +E     SL++LGSV
Sbjct: 311 SIMFEGVPTYPDAGRFWAIVDKYQVNQFYTAPTAIRALEAHGTKPIEPYKLDSLKVLGSV 370

Query: 387 GEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISPLPGATALKPGSATRPFFGVVP 446
           GEPIN EAW WY+ +VGK RCPIVDTWWQTETGG+++SP+ G T  KP  AT P  GV  
Sbjct: 371 GEPINEEAWHWYHTHVGKNRCPIVDTWWQTETGGIMVSPIAGITPNKPAYATMPLPGVQL 430

Query: 447 ALVDNLGNLIEG-AAEGNLVILDSWPGQARTLYGDHDRFVDTYFKTFSGMYFTGDGARRD 505
           A+VD  G  ++G A EGNL I   WPG  RT YGDHDR   TYF  + GMYFTGDG +RD
Sbjct: 431 AIVDPEGKELKGKAVEGNLCIKFPWPGMLRTTYGDHDRCKQTYFSAYPGMYFTGDGVKRD 490

Query: 506 EDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAAVVGVPHDIKGQGIYVYVTL 565
            DGYY I GRVDDV+NVSGHRMGTAEIE+A+  HPKV E+AVVG PH++KGQGIY YV  
Sbjct: 491 HDGYYRILGRVDDVINVSGHRMGTAEIENAINEHPKVIESAVVGYPHEVKGQGIYAYVIC 550

Query: 566 NAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIATAEYDG 625
           +    T E L  E+K+ + K IGPIA PD IQ  PGLPKTRSGKIMRRILRK+A   +D 
Sbjct: 551 DLKNRTEENLIGEIKDTITKSIGPIAKPDKIQIVPGLPKTRSGKIMRRILRKVAEGSFDN 610

Query: 626 LGDISTLADPGVVAHLIE 643
           +GD STL DP VV  +IE
Sbjct: 611 MGDTSTLLDPAVVEEIIE 628


Lambda     K      H
   0.318    0.135    0.418 

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: 1327
Number of extensions: 59
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: 651
Length of database: 632
Length adjustment: 38
Effective length of query: 613
Effective length of database: 594
Effective search space:   364122
Effective search space used:   364122
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 Echvi_1268 Echvi_1268 (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.28349.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   9.8e-294  961.3   1.0   1.1e-293  961.1   1.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_1268  Echvi_1268 acetate--CoA ligase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_1268  Echvi_1268 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  961.1   1.0  1.1e-293  1.1e-293       4     628 ..       8     628 ..       5     629 .. 0.98

  Alignments for each domain:
  == domain 1  score: 961.1 bits;  conditional E-value: 1.1e-293
                            TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkvai 76 
                                          l+ y + y++++++pe+fwa+ a  +++w+k ++kvl++++e  +vkWf++g++n++ n ++rh+    d+ ai
  lcl|FitnessBrowser__Cola:Echvi_1268   8 LSGYFHEYQKSVTEPEQFWARIAD-SFHWKKRWDKVLEWDFEGpDVKWFVNGKVNITENILERHLFIMGDRPAI 80 
                                          6678899****************9.6***************988****************************** PP

                            TIGR02188  77 iwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsa 150
                                          iwe ++++e+ r+ltY++l++evc+++n+lk+ G+ kgd+v+iY+pm+pea+iamlacaRiGavhsvvfaGfs+
  lcl|FitnessBrowser__Cola:Echvi_1268  81 IWEPNDPNEEGRTLTYRQLYHEVCKFSNALKAKGIGKGDKVIIYMPMVPEAAIAMLACARIGAVHSVVFAGFSS 154
                                          ************************************************************************** PP

                            TIGR02188 151 ealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelve 224
                                          +ala+Ri+d+eak v+t+d+++Rg k+i++k+ vdealek++ ++e+v+v++rt++ev+ ++egrD+ww+++++
  lcl|FitnessBrowser__Cola:Echvi_1268 155 SALADRINDCEAKAVLTSDGNFRGTKKIAVKDLVDEALEKTK-TIETVIVYQRTKQEVK-MVEGRDIWWHDAID 226
                                          ****************************************98.7*************76.************** PP

                            TIGR02188 225 keasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsY 298
                                           +++++ e+e +dsed+lfiLYtsGstGkPkGv+httgGy+++ ++t++ vf++ ++d++wCtaD+GW+tGhsY
  lcl|FitnessBrowser__Cola:Echvi_1268 227 -GQPDTNEAEVMDSEDMLFILYTSGSTGKPKGVVHTTGGYMVYSKYTFENVFQYSPGDVYWCTADIGWITGHSY 299
                                          .6************************************************************************ PP

                            TIGR02188 299 ivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGep 372
                                          ivygPL++Gat+++fegvptypda+rfw++++ky+v++fYtaPtaiRal + g++ ++ ++l+sl+vlgsvGep
  lcl|FitnessBrowser__Cola:Echvi_1268 300 IVYGPLLAGATSIMFEGVPTYPDAGRFWAIVDKYQVNQFYTAPTAIRALEAHGTKPIEPYKLDSLKVLGSVGEP 373
                                          ************************************************************************** PP

                            TIGR02188 373 inpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeg 446
                                          in eaw+Wy+++vGk++cpivdtwWqtetGgi+++p++g +t+ kp+ at+Pl+G++ ++vd egke++ ++ +
  lcl|FitnessBrowser__Cola:Echvi_1268 374 INEEAWHWYHTHVGKNRCPIVDTWWQTETGGIMVSPIAG-ITPNKPAYATMPLPGVQLAIVDPEGKELKGKAVE 446
                                          ***************************************.5****************************77777 PP

                            TIGR02188 447 gvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesa 520
                                          g L+ik pwP+mlrt ygd++r  +tYf++++g+yftGDg++rd+dGy+ ilGRvDdvinvsGhr+gtaeie+a
  lcl|FitnessBrowser__Cola:Echvi_1268 447 GNLCIKFPWPGMLRTTYGDHDRCKQTYFSAYPGMYFTGDGVKRDHDGYYRILGRVDDVINVSGHRMGTAEIENA 520
                                          9************************************************************************* PP

                            TIGR02188 521 lvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsG 594
                                          + +h++v e+avvg+p+e+kg+ i+a+v+   +++++e +l  e+k++++k+igpiakpdki++v+ lPktRsG
  lcl|FitnessBrowser__Cola:Echvi_1268 521 INEHPKVIESAVVGYPHEVKGQGIYAYVICDLKNRTEE-NLIGEIKDTITKSIGPIAKPDKIQIVPGLPKTRSG 593
                                          ******************************99999888.5********************************** PP

                            TIGR02188 595 kimRRllrkiaege.ellgdvstledpsvveelke 628
                                          kimRR+lrk+aeg+ +++gd+stl dp+vvee++e
  lcl|FitnessBrowser__Cola:Echvi_1268 594 KIMRRILRKVAEGSfDNMGDTSTLLDPAVVEEIIE 628
                                          ********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (632 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: 11.72
//
[ok]

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

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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 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