GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF398
          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.3025312.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 28.47
//
[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