GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS17345
          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.5230.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.81
//
[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