Alignments for a candidate for aceA in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Paraburkholderia bryophila 376MFSha3.1

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate H281DRAFT_00580 H281DRAFT_00580 isocitrate lyase

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



>FitnessBrowser__Burk376:H281DRAFT_00580
          Length = 435

 Score =  645 bits (1663), Expect = 0.0
 Identities = 318/437 (72%), Positives = 366/437 (83%), Gaps = 10/437 (2%)

Query: 4   TREQQIAALEKDWAENPRWKGVTRNYSAADVVRLRGSVQPEHTFAKMGADKLWNLVTQGA 63
           TRE+Q   L++ W  +PRWKGV R+Y+A DV+RLRGSVQ EHT AK GA+KLW+ V    
Sbjct: 3   TREEQARQLQQQWETDPRWKGVKRSYTAEDVIRLRGSVQVEHTLAKRGAEKLWHSVNT-- 60

Query: 64  KPSFRPEKDFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLYPVD 123
                  + FVN +GALTG QA+QQVKAG++AIYLSGWQVA D N A  MYPDQSLYP +
Sbjct: 61  -------EPFVNSLGALTGNQAMQQVKAGLKAIYLSGWQVAGDANVAGEMYPDQSLYPAN 113

Query: 124 SVPTVVKRINNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELMKSM 183
           SVP VVKRINN+  RADQIQW  GKNPGDEGYIDYFAPIVADAEAGFGGVLNA+ELMK+M
Sbjct: 114 SVPLVVKRINNTLTRADQIQWSEGKNPGDEGYIDYFAPIVADAEAGFGGVLNAFELMKAM 173

Query: 184 IEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGTPTIILARTDA 243
           IEAGAAGVHFEDQLASVKKCGHMGGKVLVPT+E V KLTAARLAADV+G  T++LARTDA
Sbjct: 174 IEAGAAGVHFEDQLASVKKCGHMGGKVLVPTRENVAKLTAARLAADVSGVSTVLLARTDA 233

Query: 244 NAADLLTSDCDPYDQPFVTGERTQEGFYKVRAGLDQAIARGLAYAPFADLIWCETAKPDL 303
            AADL+TSD D  D+PF+TGERT EGFY+ + GL+QAI+RGLAYAP+AD+IWCET KPDL
Sbjct: 234 EAADLITSDVDENDKPFLTGERTVEGFYRTKPGLEQAISRGLAYAPYADMIWCETGKPDL 293

Query: 304 DEARRFAEAIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITLAGI 363
           + A++FA+AI KEYPDQLLSYNCSPSFNWKKNLDDATIAKFQREL AMGYK QFITLAG 
Sbjct: 294 EFAKKFADAIHKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELGAMGYKFQFITLAGF 353

Query: 364 HNMWHSMFNLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTVIQG 423
           H + +SMFNLAH YARN MTA+V++Q+ EFA A KG+T V HQ+EVGTGYFD +T  ++ 
Sbjct: 354 HALNYSMFNLAHGYARNQMTAFVEMQQAEFAAAEKGFTAVKHQREVGTGYFDAVTQTVE- 412

Query: 424 GTSSVTALTGSTEEEQF 440
             +S TAL GSTE+EQF
Sbjct: 413 REASTTALHGSTEDEQF 429


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: 683
Number of extensions: 13
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: 435
Length adjustment: 32
Effective length of query: 409
Effective length of database: 403
Effective search space:   164827
Effective search space used:   164827
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 H281DRAFT_00580 H281DRAFT_00580 (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.23206.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   6.3e-196  637.7   6.0   1.5e-115  372.5   0.1    2.0  2  lcl|FitnessBrowser__Burk376:H281DRAFT_00580  H281DRAFT_00580 isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00580  H281DRAFT_00580 isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.5   0.1  1.5e-115  1.5e-115       2     254 ..       9     253 ..       8     254 .. 0.98
   2 !  268.3   1.9   5.8e-84   5.8e-84     353     527 .]     254     429 ..     252     429 .. 0.99

  Alignments for each domain:
  == domain 1  score: 372.5 bits;  conditional E-value: 1.5e-115
                                    TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGal 67 
                                                  +++q++W+td+rw+++kr y+a+dv++lrGsv+ e++l++++a+klw+ +++e      +++lGal
  lcl|FitnessBrowser__Burk376:H281DRAFT_00580   9 RQLQQQWETDPRWKGVKRSYTAEDVIRLRGSVQVEHTLAKRGAEKLWHSVNTEP----FVNSLGAL 70 
                                                  579**********************************************99876....59****** PP

                                    TIGR01346  68 dpvqvsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkea 132
                                                  +++q++qq+ka l+a+ylsGWqv++dan+++e++Pd+++yPa++vP +v+r++++l ++d++q+++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00580  71 TGNQAMQQVKAgLKAIYLSGWQVAGDANVAGEMYPDQSLYPANSVPLVVKRINNTLTRADQIQWSE 136
                                                  ****************************************************************** PP

                                    TIGR01346 133 rskakdeeelkelyidylvPivadadaGfGGvlavfkltkllierGaagvhledqlssekkCGhla 198
                                                  ++++ de      yidy+ Pivada+aGfGGvl++f+l+k++ie+Gaagvh+edql+s+kkCGh++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00580 137 GKNPGDE-----GYIDYFAPIVADAEAGFGGVLNAFELMKAMIEAGAAGVHFEDQLASVKKCGHMG 197
                                                  ****999.....7***************************************************** PP

                                    TIGR01346 199 GkvlvpvqehvnrlvaarlaadvmgvetllvartdaeaatlitsdvdardhefivG 254
                                                  Gkvlvp++e+v +l aarlaadv gv t+l+artdaeaa+litsdvd+ d++f++G
  lcl|FitnessBrowser__Burk376:H281DRAFT_00580 198 GKVLVPTRENVAKLTAARLAADVSGVSTVLLARTDAEAADLITSDVDENDKPFLTG 253
                                                  *******************************************************9 PP

  == domain 2  score: 268.3 bits;  conditional E-value: 5.8e-84
                                    TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPs 418
                                                  ert eGfyr+k g+e+ai+r+ a+aPyad++W+et++Pdle ak+fa+++++++Pd+ll+yn+sPs
  lcl|FitnessBrowser__Burk376:H281DRAFT_00580 254 ERTVEGFYRTKPGLEQAISRGLAYAPYADMIWCETGKPDLEFAKKFADAIHKEYPDQLLSYNCSPS 319
                                                  8***************************************************************** PP

                                    TIGR01346 419 fnWdkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvqqrel. 483
                                                  fnW+k+l+d +i+kf++elg++GykfqfitlaG+h+ ++++f+la+++a++ m+a+ve +qq e+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_00580 320 FNWKKNLDDATIAKFQRELGAMGYKFQFITLAGFHALNYSMFNLAHGYARNQMTAFVE-MQQAEFa 384
                                                  **********************************************************.******9 PP

                                    TIGR01346 484 ..edGvdvlkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                                    e+G++++khq+e+G++yfd ++++v+   ++t+al++s+e++qf
  lcl|FitnessBrowser__Burk376:H281DRAFT_00580 385 aaEKGFTAVKHQREVGTGYFDAVTQTVER-EASTTALHGSTEDEQF 429
                                                  999*************************9.8999***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (435 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: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 4.60
//
[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