Alignments for a candidate for acs in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Pseudomonas simiae WCS417

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate GFF4676 PS417_23925 acetyl-CoA synthetase

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



>FitnessBrowser__WCS417:GFF4676
          Length = 645

 Score =  816 bits (2107), Expect = 0.0
 Identities = 398/640 (62%), Positives = 476/640 (74%), Gaps = 5/640 (0%)

Query: 5   SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63
           S +P    V  +    +  YK +Y+QS+  PD FW EQAK  LDWI P+ TV+++  +  
Sbjct: 5   STFPTADAVRRAAQLSQEDYKRLYRQSIEQPDTFWAEQAKGFLDWITPWHTVQRSDINTG 64

Query: 64  HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
                WFA G LNVSYNC+DRHLA+R +Q A IWEGDDP++S  ITYR+LH+ V + AN 
Sbjct: 65  AAH--WFAGGQLNVSYNCIDRHLAQRAEQPAFIWEGDDPAKSCKITYRQLHQNVSRLANV 122

Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
           L+ + V +GD V IYMPMIPEA  AMLACTRIGA+HSVVFGGFSP+AL  RI D   + V
Sbjct: 123 LKSRGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSVVFGGFSPDALRDRIQDADCRTV 182

Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243
           ITADEGVR GK + LK NVD AL +    ++  V+V +RT   + W++ RD+ Y+  +  
Sbjct: 183 ITADEGVRGGKPVALKQNVDKALAS--CPNVSTVLVVERTGATVNWSEGRDLKYQQALDA 240

Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303
           A   C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + V DY+ GEV+WC
Sbjct: 241 ASDNCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDGEVFWC 300

Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363
           TADVGWVTGHSYIVYGPLANGAT+L+FEGVP+YPD +R  +VIDKHKV+I YTAPTA+RA
Sbjct: 301 TADVGWVTGHSYIVYGPLANGATSLMFEGVPSYPDSSRFWQVIDKHKVNIFYTAPTALRA 360

Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423
           +M  G A +E    +SLRLLGSVGEPINPEAWDWY+  VG++RCPIVDTWWQTETGG+++
Sbjct: 361 LMREGHAPLESTSRASLRLLGSVGEPINPEAWDWYFNAVGEQRCPIVDTWWQTETGGIML 420

Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483
           SPL  A  +KPG AT+P FGV P L+D  G    GA  G L I  SWPGQ R++YGD  R
Sbjct: 421 SPLVSAQRIKPGCATQPMFGVQPVLLDEQGKEFSGAGSGVLAIKASWPGQIRSVYGDPQR 480

Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543
            +DTYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H  VA
Sbjct: 481 MIDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDLVA 540

Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603
           EAAVVG PHD+KGQGIY +VT   G E  +AL+  L   V KEIG  A P++IQWAP LP
Sbjct: 541 EAAVVGYPHDVKGQGIYAFVTPMNGVEPDDALKRHLLELVSKEIGSFAKPELIQWAPALP 600

Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           KTRSGKIMRRILRKIA  E D LGD STLADP VV  LI+
Sbjct: 601 KTRSGKIMRRILRKIACNELDSLGDTSTLADPSVVEGLID 640


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: 1340
Number of extensions: 63
Number of successful extensions: 3
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: 645
Length adjustment: 38
Effective length of query: 613
Effective length of database: 607
Effective search space:   372091
Effective search space used:   372091
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 GFF4676 PS417_23925 (acetyl-CoA synthetase)
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.16939.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 1017.0   0.0          0 1016.7   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF4676  PS417_23925 acetyl-CoA synthetas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4676  PS417_23925 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1016.7   0.0         0         0       3     628 ..      20     640 ..      18     641 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1016.7 bits;  conditional E-value: 0
                           TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkvai 76 
                                         ++e+yk+ly+++ie+p++fwa++ak  l+w++p+++v++++ ++  ++Wf++g+lnvsync+drh+++r+++ a 
  lcl|FitnessBrowser__WCS417:GFF4676  20 SQEDYKRLYRQSIEQPDTFWAEQAKGFLDWITPWHTVQRSDINTgAAHWFAGGQLNVSYNCIDRHLAQRAEQPAF 94 
                                         5789*************************************99999***************************** PP

                           TIGR02188  77 iwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsae 151
                                         iwegd++ + s k+tY++l+++v+rlanvlk+ Gvkkgdrv+iY+pmipea++amlac+RiGavhsvvf+Gfs++
  lcl|FitnessBrowser__WCS417:GFF4676  95 IWEGDDPAK-SCKITYRQLHQNVSRLANVLKSRGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSVVFGGFSPD 168
                                         *******96.9**************************************************************** PP

                           TIGR02188 152 alaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelveke 226
                                         al++Ri+da++++vitadeg+Rggk ++lk++vd+al++++ +v++vlvv+rtg+ v+ w+egrD++++++++  
  lcl|FitnessBrowser__WCS417:GFF4676 169 ALRDRIQDADCRTVITADEGVRGGKPVALKQNVDKALASCP-NVSTVLVVERTGATVN-WSEGRDLKYQQALDA- 240
                                         ****************************************9.6*************66.**************5. PP

                           TIGR02188 227 asaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivy 301
                                         as++c+pe++d+edplfiLYtsGstGkPkGvlhttgGyll+aa+t+kyv d++d+++fwCtaDvGWvtGhsYivy
  lcl|FitnessBrowser__WCS417:GFF4676 241 ASDNCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDGEVFWCTADVGWVTGHSYIVY 315
                                         *************************************************************************** PP

                           TIGR02188 302 gPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpe 376
                                         gPLanGat+l+fegvp+ypd+srfw+vi+k+kv+ifYtaPta+Ralm++g++ ++++++ slr+lgsvGepinpe
  lcl|FitnessBrowser__WCS417:GFF4676 316 GPLANGATSLMFEGVPSYPDSSRFWQVIDKHKVNIFYTAPTALRALMREGHAPLESTSRASLRLLGSVGEPINPE 390
                                         *************************************************************************** PP

                           TIGR02188 377 aweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvi 451
                                         aw+Wy++ vG+++cpivdtwWqtetGgi+++pl + a  +kpg+at+P+fG++++++de+gke++   + gvL+i
  lcl|FitnessBrowser__WCS417:GFF4676 391 AWDWYFNAVGEQRCPIVDTWWQTETGGIMLSPLVS-AQRIKPGCATQPMFGVQPVLLDEQGKEFSGAGS-GVLAI 463
                                         ***********************************.6***************************98777.8**** PP

                           TIGR02188 452 kkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvshea 526
                                         k +wP+++r++ygd++r+++tYfk ++g+yftGDgarrd+dG++wi+GR+DdvinvsGhr+gtae+esalv h+ 
  lcl|FitnessBrowser__WCS417:GFF4676 464 KASWPGQIRSVYGDPQRMIDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDL 538
                                         *************************************************************************** PP

                           TIGR02188 527 vaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRll 601
                                         vaeaavvg+p+++kg+ i+afv+ ++gve+d+ +l+++l +lv+keig++akp+ i+++++lPktRsGkimRR+l
  lcl|FitnessBrowser__WCS417:GFF4676 539 VAEAAVVGYPHDVKGQGIYAFVTPMNGVEPDD-ALKRHLLELVSKEIGSFAKPELIQWAPALPKTRSGKIMRRIL 612
                                         ********************************.5***************************************** PP

                           TIGR02188 602 rkiaege.ellgdvstledpsvveelke 628
                                         rkia +e ++lgd+stl+dpsvve l++
  lcl|FitnessBrowser__WCS417:GFF4676 613 RKIACNElDSLGDTSTLADPSVVEGLID 640
                                         ************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (645 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: 10.79
//
[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:

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