GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Marinobacter adhaerens HP15

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate GFF2751 HP15_2695 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-15952
         (401 letters)



>FitnessBrowser__Marino:GFF2751
          Length = 415

 Score =  592 bits (1525), Expect = e-174
 Identities = 302/406 (74%), Positives = 344/406 (84%), Gaps = 6/406 (1%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           + +A I+DA+RTPIGRY GAL++VRADDLGAIP+KAL  R+P LDWS +DDV+YGCANQA
Sbjct: 7   LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNR+VARM+ LLAGLPV VPG+T+NRLCGSG+DAVGSAARA+R GE  LM+AGGVESM
Sbjct: 67  GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           SRAPFVMGK++ AF R AEIFDTTIGWRFVN ++++ +GIDSMPETAENVAA F ISR D
Sbjct: 127 SRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISRED 186

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QDAFALRSQ + AAA   GRLA EI  V I +RK    +V+ DEHPR +T+LE+LA L T
Sbjct: 187 QDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPR-ETSLEKLASLPT 245

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
           PFR+ G+VTAGNASGVNDGACALLLA ++A +++ LK RARVV MATAGVEPRIMG GP 
Sbjct: 246 PFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPA 305

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PATRKVL   GL LADMDVIELNEAFAAQ LAV R+LGL DD E VNPNGGAIALGHPLG
Sbjct: 306 PATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLG 365

Query: 361 MSGARLVTTALHELEER-----QGRYALCTMCIGVGQGIALIIERI 401
           MSGARLVTTAL+ELE R     + RYALCTMCIGVGQGIALIIER+
Sbjct: 366 MSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERM 411


Lambda     K      H
   0.319    0.134    0.384 

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: 580
Number of extensions: 14
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: 401
Length of database: 415
Length adjustment: 31
Effective length of query: 370
Effective length of database: 384
Effective search space:   142080
Effective search space used:   142080
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 GFF2751 HP15_2695 (acetyl-CoA acetyltransferase)
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.29347.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.8e-223  727.7   6.0   2.1e-223  727.5   6.0    1.0  1  lcl|FitnessBrowser__Marino:GFF2751  HP15_2695 acetyl-CoA acetyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2751  HP15_2695 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  727.5   6.0  2.1e-223  2.1e-223       1     400 []       8     411 ..       8     411 .. 0.98

  Alignments for each domain:
  == domain 1  score: 727.5 bits;  conditional E-value: 2.1e-223
                           TIGR02430   1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaallaG 75 
                                         k++yivdairtpiGrygG+ls+vraddl+a+p+kal +r+p+ld+++iddv++GcanqaGednr+varm++llaG
  lcl|FitnessBrowser__Marino:GFF2751   8 KDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQAGEDNRDVARMSLLLAG 82 
                                         689************************************************************************ PP

                           TIGR02430  76 lpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwrfvn 150
                                         lpv+vpg+t+nrlcgsg+da+g aarai++Ge++l+iaGGvesmsrapfv+Gkadsafsr+a+++dttiGwrfvn
  lcl|FitnessBrowser__Marino:GFF2751  83 LPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESMSRAPFVMGKADSAFSRKAEIFDTTIGWRFVN 157
                                         *************************************************************************** PP

                           TIGR02430 151 pklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvdkdehl 225
                                         p lk++yG+dsmpetaenva +fg+sredqdafalrsqqrtaaaq++G +a+ei+pv+i+++k ++ vvd+deh+
  lcl|FitnessBrowser__Marino:GFF2751 158 PVLKKQYGIDSMPETAENVAADFGISREDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHP 232
                                         *************************************************************************** PP

                           TIGR02430 226 raettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprvmGlgpvp 300
                                         r et+le+la l +++re+gtvtaGnasGvndGa+allla+++a+k+++l+prar++a+a+aGvepr+mG+gp+p
  lcl|FitnessBrowser__Marino:GFF2751 233 R-ETSLEKLASLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPAP 306
                                         *.************************************************************************* PP

                           TIGR02430 301 avkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlvltalkqlek 375
                                         a++k+la agl+l+d+dvielneafaaqalav+r+lgl+dd+++vnpnGGaialGhplG+sGarlv+tal++le+
  lcl|FitnessBrowser__Marino:GFF2751 307 ATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLGMSGARLVTTALNELER 381
                                         *************************************************************************98 PP

                           TIGR02430 376 s.....ggryalatlciGvGqGialvierv 400
                                         +     + ryal+t+ciGvGqGial+ier+
  lcl|FitnessBrowser__Marino:GFF2751 382 RhaagqKARYALCTMCIGVGQGIALIIERM 411
                                         633222469*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (415 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.60
//
[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