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.11390.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: 12.12
//
[ok]

This GapMind analysis is from Sep 17 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:

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:

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:

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:

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