Alignments for a candidate for aceA in Burkholderia vietnamiensis G4

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Burkholderia vietnamiensis G4

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_011885172.1 isocitrate lyase

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



>NCBI__GCF_000016205.1:WP_011885172.1
          Length = 435

 Score =  629 bits (1623), Expect = 0.0
 Identities = 305/438 (69%), Positives = 364/438 (83%), Gaps = 10/438 (2%)

Query: 3   LTREQQIAALEKDWAENPRWKGVTRNYSAADVVRLRGSVQPEHTFAKMGADKLWNLVTQG 62
           ++R+QQ   L+K W  +PRW G+ R Y+A DVVRLRGS+  EHT AK GA+KLW L+   
Sbjct: 1   MSRQQQALELQKQWDTDPRWTGIKRGYTADDVVRLRGSIAVEHTLAKRGAEKLWRLIN-- 58

Query: 63  AKPSFRPEKDFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLYPV 122
                  E+ FVN +GALTG QA+QQVKAG++AIYLSGWQVA D N A  MYPDQSLYP 
Sbjct: 59  -------EEPFVNALGALTGNQAMQQVKAGLKAIYLSGWQVAGDANVAGEMYPDQSLYPA 111

Query: 123 DSVPTVVKRINNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELMKS 182
           +SVP VVKRINN+  RADQIQW  GKNPGD+GY+D+FAPIVADAEAGFGGVLNA+ELMK+
Sbjct: 112 NSVPLVVKRINNTLTRADQIQWSEGKNPGDDGYVDFFAPIVADAEAGFGGVLNAFELMKA 171

Query: 183 MIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGTPTIILARTD 242
           MIEAGA+GVHFEDQLASVKKCGHMGGKVLVPT+EAV KL+AARLAADV GTPT+++ARTD
Sbjct: 172 MIEAGASGVHFEDQLASVKKCGHMGGKVLVPTREAVAKLSAARLAADVMGTPTVLVARTD 231

Query: 243 ANAADLLTSDCDPYDQPFVTGERTQEGFYKVRAGLDQAIARGLAYAPFADLIWCETAKPD 302
           A AADL+TSD D  D+PF+TGERT EGF++ + GL+QAI+RGLAYAP+ADL+WCET KPD
Sbjct: 232 AEAADLITSDIDDNDKPFLTGERTVEGFFRTKPGLEQAISRGLAYAPYADLVWCETGKPD 291

Query: 303 LDEARRFAEAIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITLAG 362
           L+ A++FAEAI K++P ++LSYNCSPSFNWKKNLDDATIAKFQ+EL AMGYK QFITLAG
Sbjct: 292 LEYAKKFAEAIHKQFPGKMLSYNCSPSFNWKKNLDDATIAKFQKELGAMGYKFQFITLAG 351

Query: 363 IHNMWHSMFNLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTVIQ 422
            H + +SMFNLAH YAR  M+A+V+LQ+ EF  A KG+T V HQ+EVGTGYFD +T  ++
Sbjct: 352 FHALNYSMFNLAHGYARTQMSAFVELQQAEFEAADKGFTAVKHQREVGTGYFDAVTQTVE 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: 682
Number of extensions: 19
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 WP_011885172.1 (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.2108.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-196  639.2   4.5   2.4e-116  375.1   0.1    2.0  2  lcl|NCBI__GCF_000016205.1:WP_011885172.1  isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016205.1:WP_011885172.1  isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.1   0.1  2.4e-116  2.4e-116       3     254 ..       9     252 ..       7     253 .. 0.98
   2 !  266.0   1.4   2.8e-83   2.8e-83     353     527 .]     253     428 ..     252     428 .. 0.99

  Alignments for each domain:
  == domain 1  score: 375.1 bits;  conditional E-value: 2.4e-116
                                 TIGR01346   3 eiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpvq 71 
                                               e+qk+Wdtd+rw +ikr y+a+dvv+lrGs+  e++l++++a+klwr++++e      +++lGal+++q
  lcl|NCBI__GCF_000016205.1:WP_011885172.1   9 ELQKQWDTDPRWTGIKRGYTADDVVRLRGSIAVEHTLAKRGAEKLWRLINEEP----FVNALGALTGNQ 73 
                                               99**********************************************98765....69********** PP

                                 TIGR01346  72 vsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakde 139
                                               ++qq+ka l+a+ylsGWqv++dan+++e++Pd+++yPa++vP +v+r++++l ++d++q+++++++ d+
  lcl|NCBI__GCF_000016205.1:WP_011885172.1  74 AMQQVKAgLKAIYLSGWQVAGDANVAGEMYPDQSLYPANSVPLVVKRINNTLTRADQIQWSEGKNPGDD 142
                                               ******************************************************************999 PP

                                 TIGR01346 140 eelkelyidylvPivadadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqeh 208
                                                     y+d++ Pivada+aGfGGvl++f+l+k++ie+Ga+gvh+edql+s+kkCGh++Gkvlvp++e+
  lcl|NCBI__GCF_000016205.1:WP_011885172.1 143 -----GYVDFFAPIVADAEAGFGGVLNAFELMKAMIEAGASGVHFEDQLASVKKCGHMGGKVLVPTREA 206
                                               .....7*************************************************************** PP

                                 TIGR01346 209 vnrlvaarlaadvmgvetllvartdaeaatlitsdvdardhefivG 254
                                               v +l aarlaadvmg++t+lvartdaeaa+litsd+d+ d++f++G
  lcl|NCBI__GCF_000016205.1:WP_011885172.1 207 VAKLSAARLAADVMGTPTVLVARTDAEAADLITSDIDDNDKPFLTG 252
                                               *********************************************9 PP

  == domain 2  score: 266.0 bits;  conditional E-value: 2.8e-83
                                 TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnW 421
                                               ert eGf+r+k g+e+ai+r+ a+aPyadlvW+et++Pdle ak+fae+++++fP+k+l+yn+sPsfnW
  lcl|NCBI__GCF_000016205.1:WP_011885172.1 253 ERTVEGFFRTKPGLEQAISRGLAYAPYADLVWCETGKPDLEYAKKFAEAIHKQFPGKMLSYNCSPSFNW 321
                                               7******************************************************************** PP

                                 TIGR01346 422 dkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvqqrel...edGv 487
                                               +k+l+d +i+kf+kelg++GykfqfitlaG+h+ ++++f+la+++a+  m a+ve +qq e+   ++G+
  lcl|NCBI__GCF_000016205.1:WP_011885172.1 322 KKNLDDATIAKFQKELGAMGYKFQFITLAGFHALNYSMFNLAHGYARTQMSAFVE-LQQAEFeaaDKGF 389
                                               *******************************************************.******99999** PP

                                 TIGR01346 488 dvlkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                               +++khq+e+G++yfd ++++v+   ++t+al++s+e++qf
  lcl|NCBI__GCF_000016205.1:WP_011885172.1 390 TAVKHQREVGTGYFDAVTQTVER-EASTTALHGSTEDEQF 428
                                               **********************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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 4.19
//
[ok]

This GapMind analysis is from Apr 10 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