GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaJ2 in Phaeobacter inhibens BS107

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate GFF398 PGA1_c04090 beta-ketoadipyl-CoA thiolase PaaJ

Query= uniprot:D8ITH5
         (401 letters)



>lcl|FitnessBrowser__Phaeo:GFF398 PGA1_c04090 beta-ketoadipyl-CoA
           thiolase PaaJ
          Length = 400

 Score =  560 bits (1442), Expect = e-164
 Identities = 278/400 (69%), Positives = 321/400 (80%)

Query: 1   MEALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAG 60
           M+A ICDA RTP GRYGGAL  +R DDLAA PI +L  RNP VDWS ++D++ G ANQAG
Sbjct: 1   MDAFICDATRTPIGRYGGALSQLRTDDLAALPIAALAARNPDVDWSSLDDVILGDANQAG 60

Query: 61  EDNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMT 120
           E NRNVARMA LLAGLP  VPG+T+NRLC S +DAVGMA+R IK+G+  + IAGGVESM+
Sbjct: 61  ESNRNVARMAALLAGLPTTVPGTTINRLCASGMDAVGMASRGIKAGDYDMAIAGGVESMS 120

Query: 121 RAPFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ 180
           RAPFVM KA SAF R+ A++DTTIGWRFVN  M   YG DSMP+TA+NVA D+ I+R DQ
Sbjct: 121 RAPFVMPKATSAFTRANAVYDTTIGWRFVNKKMHEMYGTDSMPQTADNVAEDYGISREDQ 180

Query: 181 DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGV 240
           DAFA RSQ RWAAA  AG F  EI P+TIPQ+KGD LVV TDEHPRP T+   LA LKGV
Sbjct: 181 DAFAARSQARWAAAHEAGIFNDEITPVTIPQRKGDDLVVDTDEHPRPGTSAEKLAGLKGV 240

Query: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300
             PD +VTAGNASGVNDGA A+L+A+  AA    LKP AR++GM  AGV PRIMG GP P
Sbjct: 241 NGPDKSVTAGNASGVNDGAAAILMANEAAAAKNGLKPMARIVGMTAAGVEPRIMGIGPVP 300

Query: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360
           A RKVLA+ GLT+ QMDVIELNEAFA+QGLA +R+LG+ DDA HVNPNGGAIA+GHPLG 
Sbjct: 301 ATRKVLARTGLTIDQMDVIELNEAFASQGLATLRELGVADDAPHVNPNGGAIALGHPLGM 360

Query: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400
           SGARLV TA  QL+R+GGRYALCTMC+GVGQG AL++ERV
Sbjct: 361 SGARLVLTAAYQLQRTGGRYALCTMCVGVGQGTALILERV 400


Lambda     K      H
   0.320    0.135    0.394 

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: 553
Number of extensions: 16
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: 401
Length of database: 400
Length adjustment: 31
Effective length of query: 370
Effective length of database: 369
Effective search space:   136530
Effective search space used:   136530
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate GFF398 PGA1_c04090 (beta-ketoadipyl-CoA thiolase PaaJ)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

# 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/TIGR02430.hmm
# target sequence database:        /tmp/gapView.9040.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02430  [M=400]
Accession:   TIGR02430
Description: pcaF: 3-oxoadipyl-CoA thiolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.1e-212  691.3  10.7   2.3e-212  691.1  10.7    1.0  1  lcl|FitnessBrowser__Phaeo:GFF398  PGA1_c04090 beta-ketoadipyl-CoA 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF398  PGA1_c04090 beta-ketoadipyl-CoA thiolase PaaJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  691.1  10.7  2.3e-212  2.3e-212       2     400 .]       2     400 .]       1     400 [] 1.00

  Alignments for each domain:
  == domain 1  score: 691.1 bits;  conditional E-value: 2.3e-212
                         TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaallaGlpv 78 
                                       +++i+da rtpiGrygG+ls++r+ddlaa+p++al arnp++d++++ddvilG anqaGe nrnvarmaallaGlp+
  lcl|FitnessBrowser__Phaeo:GFF398   2 DAFICDATRTPIGRYGGALSQLRTDDLAALPIAALAARNPDVDWSSLDDVILGDANQAGESNRNVARMAALLAGLPT 78 
                                       69*************************************************************************** PP

                         TIGR02430  79 svpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwrfvnpklka 155
                                       +vpgtt+nrlc+sg+da+g+a r+ikaG+ d+ iaGGvesmsrapfv+ ka saf+r + + dttiGwrfvn k+++
  lcl|FitnessBrowser__Phaeo:GFF398  79 TVPGTTINRLCASGMDAVGMASRGIKAGDYDMAIAGGVESMSRAPFVMPKATSAFTRANAVYDTTIGWRFVNKKMHE 155
                                       ***************************************************************************** PP

                         TIGR02430 156 lyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvdkdehlraettle 232
                                       +yG+dsmp+ta+nvae++g+sredqdafa rsq+r+aaa+++G+f++ei+pv+i+q+kG++ vvd+deh+r+ t+ e
  lcl|FitnessBrowser__Phaeo:GFF398 156 MYGTDSMPQTADNVAEDYGISREDQDAFAARSQARWAAAHEAGIFNDEITPVTIPQRKGDDLVVDTDEHPRPGTSAE 232
                                       ***************************************************************************** PP

                         TIGR02430 233 alaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprvmGlgpvpavkkllara 309
                                       +la lk+v+ +d++vtaGnasGvndGaaa+l+a e a++++gl+p ari+++++aGvepr+mG+gpvpa++k+lar+
  lcl|FitnessBrowser__Phaeo:GFF398 233 KLAGLKGVNGPDKSVTAGNASGVNDGAAAILMANEAAAAKNGLKPMARIVGMTAAGVEPRIMGIGPVPATRKVLART 309
                                       ***************************************************************************** PP

                         TIGR02430 310 glsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlvltalkqleksggryalatlc 386
                                       gl+++++dvielneafa+q+la+lrelg+add+ +vnpnGGaialGhplG+sGarlvlta +ql+++ggryal+t+c
  lcl|FitnessBrowser__Phaeo:GFF398 310 GLTIDQMDVIELNEAFASQGLATLRELGVADDAPHVNPNGGAIALGHPLGMSGARLVLTAAYQLQRTGGRYALCTMC 386
                                       ***************************************************************************** PP

                         TIGR02430 387 iGvGqGialvierv 400
                                       +GvGqG al++erv
  lcl|FitnessBrowser__Phaeo:GFF398 387 VGVGQGTALILERV 400
                                       *************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (400 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: 12.06
//
[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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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