GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pcaF in Burkholderia phytofirmans PsJN

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate BPHYT_RS17345 BPHYT_RS17345 acetyl-CoA acetyltransferase

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



>lcl|FitnessBrowser__BFirm:BPHYT_RS17345 BPHYT_RS17345 acetyl-CoA
           acetyltransferase
          Length = 400

 Score =  588 bits (1516), Expect = e-173
 Identities = 295/401 (73%), Positives = 343/401 (85%), Gaps = 1/401 (0%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           MN+A I DA+RTPIGRY GAL  VRADDLGA+P+KALI R+P +DW  VDDVIYGCANQA
Sbjct: 1   MNDAFICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQA 60

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNRNVARM+ALLAGLPV  PG+T+NRLCGSG+DAVG+AARA++ GEA LM+AGGVESM
Sbjct: 61  GEDNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESM 120

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           +RAPFVMGK+  AF R A+I+DTTIGWRF+N LM++ +G+DSMPETAENVAA+F++SRAD
Sbjct: 121 TRAPFVMGKATSAFARQADIYDTTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRAD 180

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QDAFAL SQ KAA A  +G LA+EIV VEIAQ+KG       DEHPR +T+LE L KL  
Sbjct: 181 QDAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPR-ETSLESLGKLKG 239

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
             R  GSVTAGNASGVNDGACALLLA+ +AA ++GL+ RARVVGMATAGVEPRIMGIGP 
Sbjct: 240 VVRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARVVGMATAGVEPRIMGIGPA 299

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PAT+K+L+  G+ L  +DVIELNEAFA+QGLAVLR LGL DDD RVNPNGGAIALGHPLG
Sbjct: 300 PATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGHPLG 359

Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
            SGARL+TTAL++LE   GR+ALCTMCIGVGQGIAL+IER+
Sbjct: 360 ASGARLITTALYQLERTNGRFALCTMCIGVGQGIALVIERL 400


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: 572
Number of extensions: 16
Number of successful extensions: 2
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 BPHYT_RS17345 BPHYT_RS17345 (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.4299.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   8.8e-221  718.9   9.8   9.9e-221  718.7   9.8    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS17345  BPHYT_RS17345 acetyl-CoA acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS17345  BPHYT_RS17345 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  718.7   9.8  9.9e-221  9.9e-221       2     400 .]       3     400 .]       2     400 .] 1.00

  Alignments for each domain:
  == domain 1  score: 718.7 bits;  conditional E-value: 9.9e-221
                                TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaa 71 
                                              +++i+dairtpiGrygG+l  vraddl+avp+kal++rnp +d+ ++ddvi+GcanqaGednrnvarm+a
  lcl|FitnessBrowser__BFirm:BPHYT_RS17345   3 DAFICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQAGEDNRNVARMSA 72 
                                              79******************************************************************** PP

                                TIGR02430  72 llaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakled 141
                                              llaGlpv+ pg+t+nrlcgsg+da+g+aaraikaGea l+iaGGvesm+rapfv+Gka saf+r+a++ d
  lcl|FitnessBrowser__BFirm:BPHYT_RS17345  73 LLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESMTRAPFVMGKATSAFARQADIYD 142
                                              ********************************************************************** PP

                                TIGR02430 142 ttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikq 211
                                              ttiGwrf+np +k++yGvdsmpetaenva ef+vsr+dqdafal sqq++a+aq+ G +a+eiv vei+q
  lcl|FitnessBrowser__BFirm:BPHYT_RS17345 143 TTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRADQDAFALASQQKAARAQQDGTLAQEIVGVEIAQ 212
                                              ********************************************************************** PP

                                TIGR02430 212 kkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprari 281
                                              kkG+++    deh+r et+le+l klk+vvr+dg+vtaGnasGvndGa+allla ++a+ ++gl+ rar+
  lcl|FitnessBrowser__BFirm:BPHYT_RS17345 213 KKGDPVRALLDEHPR-ETSLESLGKLKGVVRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARV 281
                                              ***************.****************************************************** PP

                                TIGR02430 282 laaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGa 351
                                              +++a+aGvepr+mG+gp+pa++kll+++g++le+ldvielneafa+q+lavlr lgl+ddd rvnpnGGa
  lcl|FitnessBrowser__BFirm:BPHYT_RS17345 282 VGMATAGVEPRIMGIGPAPATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGA 351
                                              ********************************************************************** PP

                                TIGR02430 352 ialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400
                                              ialGhplGasGarl++tal+qle+++gr+al+t+ciGvGqGialvier+
  lcl|FitnessBrowser__BFirm:BPHYT_RS17345 352 IALGHPLGASGARLITTALYQLERTNGRFALCTMCIGVGQGIALVIERL 400
                                              ***********************************************96 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.97
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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