Alignments for a candidate for aceA in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Burkholderia phytofirmans PsJN

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate BPHYT_RS12285 BPHYT_RS12285 isocitrate lyase

Query= reanno::pseudo1_N1B4:Pf1N1B4_4042
         (441 letters)



>FitnessBrowser__BFirm:BPHYT_RS12285
          Length = 434

 Score =  646 bits (1667), Expect = 0.0
 Identities = 315/438 (71%), Positives = 367/438 (83%), Gaps = 10/438 (2%)

Query: 3   LTREQQIAALEKDWAENPRWKGVTRNYSAADVVRLRGSVQPEHTFAKMGADKLWNLVTQG 62
           ++R++Q+  L++ W  +PRWKGV R Y+A DV+RLRGSVQ EHT AK GA+KLW  V   
Sbjct: 1   MSRQEQVKQLQQQWETDPRWKGVKRTYTAEDVIRLRGSVQVEHTLAKRGAEKLWESVNN- 59

Query: 63  AKPSFRPEKDFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLYPV 122
                   + FVN +GALTG QA+QQVKAG++AIYLSGWQVA D N A  MYPDQSLYP 
Sbjct: 60  --------EPFVNSLGALTGNQAMQQVKAGLKAIYLSGWQVAGDANVAGEMYPDQSLYPA 111

Query: 123 DSVPTVVKRINNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELMKS 182
           +SVP VVKRINN+  RADQIQW  GKNPGDEGY+DYF PIVADAEAGFGGVLNA+ELMK+
Sbjct: 112 NSVPLVVKRINNTLTRADQIQWSEGKNPGDEGYVDYFQPIVADAEAGFGGVLNAFELMKA 171

Query: 183 MIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGTPTIILARTD 242
           MIEAGAAGVHFEDQLASVKKCGHMGGKVLVPT+E + KLTAARLAADV+GTPT++LARTD
Sbjct: 172 MIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTRENIAKLTAARLAADVSGTPTVLLARTD 231

Query: 243 ANAADLLTSDCDPYDQPFVTGERTQEGFYKVRAGLDQAIARGLAYAPFADLIWCETAKPD 302
           A AADL+TSD D  D+PF+TGERT EGFY+ + GL+QAI+RGLAYAP+AD+IWCET KPD
Sbjct: 232 AEAADLITSDIDENDKPFLTGERTVEGFYRTKPGLEQAISRGLAYAPYADMIWCETGKPD 291

Query: 303 LDEARRFAEAIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITLAG 362
           L+ A++FA+AI KEYPDQLLSYNCSPSFNWKKNLDDATIAKFQREL AMGYK QFITLAG
Sbjct: 292 LEFAKKFADAIHKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELGAMGYKFQFITLAG 351

Query: 363 IHNMWHSMFNLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTVIQ 422
            H + +SMFNLAH YARN MTA+V++Q+ EFA A KG+T V HQ+EVGTGYFD +T  ++
Sbjct: 352 FHALNYSMFNLAHGYARNQMTAFVEMQQAEFAAAEKGFTAVKHQREVGTGYFDAVTQTVE 411

Query: 423 GGTSSVTALTGSTEEEQF 440
              +S TAL GSTE+EQF
Sbjct: 412 -REASTTALHGSTEDEQF 428


Lambda     K      H
   0.317    0.131    0.393 

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: 686
Number of extensions: 15
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: 441
Length of database: 434
Length adjustment: 32
Effective length of query: 409
Effective length of database: 402
Effective search space:   164418
Effective search space used:   164418
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate BPHYT_RS12285 BPHYT_RS12285 (isocitrate lyase)
to HMM TIGR01346 (aceA: isocitrate lyase (EC 4.1.3.1))

# 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.aa/TIGR01346.hmm
# target sequence database:        /tmp/gapView.23430.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01346  [M=527]
Accession:   TIGR01346
Description: isocit_lyase: isocitrate lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.5e-196  639.8   5.1   6.9e-116  373.6   0.1    2.0  2  lcl|FitnessBrowser__BFirm:BPHYT_RS12285  BPHYT_RS12285 isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS12285  BPHYT_RS12285 isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.6   0.1  6.9e-116  6.9e-116       2     254 ..       8     252 ..       7     253 .. 0.98
   2 !  268.3   1.9   5.8e-84   5.8e-84     353     527 .]     253     428 ..     251     428 .. 0.99

  Alignments for each domain:
  == domain 1  score: 373.6 bits;  conditional E-value: 6.9e-116
                                TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpvq 71 
                                              +++q++W+td+rw+++kr y+a+dv++lrGsv+ e++l++++a+klw+ +++e      +++lGal+++q
  lcl|FitnessBrowser__BFirm:BPHYT_RS12285   8 KQLQQQWETDPRWKGVKRTYTAEDVIRLRGSVQVEHTLAKRGAEKLWESVNNE----PFVNSLGALTGNQ 73 
                                              789*********************************************99765....569********** PP

                                TIGR01346  72 vsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakdee 140
                                              ++qq+ka l+a+ylsGWqv++dan+++e++Pd+++yPa++vP +v+r++++l ++d++q+++++++ de 
  lcl|FitnessBrowser__BFirm:BPHYT_RS12285  74 AMQQVKAgLKAIYLSGWQVAGDANVAGEMYPDQSLYPANSVPLVVKRINNTLTRADQIQWSEGKNPGDE- 142
                                              ******************************************************************999. PP

                                TIGR01346 141 elkelyidylvPivadadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqehvn 210
                                                   y+dy++Pivada+aGfGGvl++f+l+k++ie+Gaagvh+edql+s+kkCGh++Gkvlvp++e++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS12285 143 ----GYVDYFQPIVADAEAGFGGVLNAFELMKAMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTRENIA 208
                                              ....7***************************************************************** PP

                                TIGR01346 211 rlvaarlaadvmgvetllvartdaeaatlitsdvdardhefivG 254
                                              +l aarlaadv g++t+l+artdaeaa+litsd+d+ d++f++G
  lcl|FitnessBrowser__BFirm:BPHYT_RS12285 209 KLTAARLAADVSGTPTVLLARTDAEAADLITSDIDENDKPFLTG 252
                                              *******************************************9 PP

  == domain 2  score: 268.3 bits;  conditional E-value: 5.8e-84
                                TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnWd 422
                                              ert eGfyr+k g+e+ai+r+ a+aPyad++W+et++Pdle ak+fa+++++++Pd+ll+yn+sPsfnW+
  lcl|FitnessBrowser__BFirm:BPHYT_RS12285 253 ERTVEGFYRTKPGLEQAISRGLAYAPYADMIWCETGKPDLEFAKKFADAIHKEYPDQLLSYNCSPSFNWK 322
                                              8********************************************************************* PP

                                TIGR01346 423 kaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvqqrel...edGvdv 489
                                              k+l+d +i+kf++elg++GykfqfitlaG+h+ ++++f+la+++a++ m+a+ve +qq e+   e+G+++
  lcl|FitnessBrowser__BFirm:BPHYT_RS12285 323 KNLDDATIAKFQRELGAMGYKFQFITLAGFHALNYSMFNLAHGYARNQMTAFVE-MQQAEFaaaEKGFTA 391
                                              ******************************************************.******9999***** PP

                                TIGR01346 490 lkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                              +khq+e+G++yfd ++++v+   ++t+al++s+e++qf
  lcl|FitnessBrowser__BFirm:BPHYT_RS12285 392 VKHQREVGTGYFDAVTQTVER-EASTTALHGSTEDEQF 428
                                              ********************9.8999***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (434 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: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 3.38
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis