Alignments for a candidate for aceA in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Stenotrophomonas chelatiphaga DSM 21508

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_057509262.1 ABB28_RS14275 isocitrate lyase

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



>NCBI__GCF_001431535.1:WP_057509262.1
          Length = 430

 Score =  607 bits (1565), Expect = e-178
 Identities = 302/429 (70%), Positives = 348/429 (81%), Gaps = 14/429 (3%)

Query: 12  LEKDWAENPRWKGVTRNYSAADVVRLRGSVQPEHTFAKMGADKLWNLVTQGAKPSFRPEK 71
           ++ DW  NPRW G+ RNY+AADVVRLRG+V  EH+ A+MGA+KLW         ++  EK
Sbjct: 10  IQHDWDTNPRWHGIERNYTAADVVRLRGTVHVEHSLARMGAEKLW---------TYLQEK 60

Query: 72  DFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLYPVDSVPTVVKR 131
           DFVN +GALTG QA+QQVKAG+ AIYLSGWQVAAD N A  MYPDQSLYP DSVP VVKR
Sbjct: 61  DFVNALGALTGNQAMQQVKAGLNAIYLSGWQVAADANLAGQMYPDQSLYPADSVPAVVKR 120

Query: 132 INNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELMKSMIEAGAAGV 191
           INN+  RADQ+    GK+      ID+  PIVADAEAGFGGVLNA+ELMK+MIEAGAAGV
Sbjct: 121 INNTLLRADQLHHAEGKDE-----IDFLQPIVADAEAGFGGVLNAFELMKAMIEAGAAGV 175

Query: 192 HFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGTPTIILARTDANAADLLTS 251
           HFEDQLASVKKCGHMGGKVLVPT+EA++KL AARLAADV G PT+++ARTDA AADLLTS
Sbjct: 176 HFEDQLASVKKCGHMGGKVLVPTREAIEKLNAARLAADVLGVPTLLVARTDAEAADLLTS 235

Query: 252 DCDPYDQPFVTGERTQEGFYKVRAGLDQAIARGLAYAPFADLIWCETAKPDLDEARRFAE 311
           D D  DQPF TGERT EGFYK R GLDQAI+RGLAYAP+ADL+WCET KPDL+ AR+FAE
Sbjct: 236 DIDANDQPFATGERTTEGFYKTRNGLDQAISRGLAYAPYADLVWCETGKPDLEFARQFAE 295

Query: 312 AIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITLAGIHNMWHSMF 371
           AI  ++P +LL+YNCSPSFNWKKNLDDATIA FQ E++  GY+ QFITLAG H + +SMF
Sbjct: 296 AIHAKFPGKLLAYNCSPSFNWKKNLDDATIATFQTEIAKYGYRFQFITLAGFHALNYSMF 355

Query: 372 NLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTVIQGGTSSVTAL 431
           NLAH YAR  M+A+V+LQE EFA A +G+T V HQ+EVGTGYFD +T  IQ G SS TAL
Sbjct: 356 NLAHGYARRQMSAFVELQEAEFAAADRGFTAVKHQREVGTGYFDAVTQAIQQGQSSTTAL 415

Query: 432 TGSTEEEQF 440
           TGSTEE QF
Sbjct: 416 TGSTEEAQF 424


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: 654
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: 430
Length adjustment: 32
Effective length of query: 409
Effective length of database: 398
Effective search space:   162782
Effective search space used:   162782
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_057509262.1 ABB28_RS14275 (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.8859.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-192  626.6   7.6   3.5e-111  358.1   0.3    2.0  2  lcl|NCBI__GCF_001431535.1:WP_057509262.1  ABB28_RS14275 isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057509262.1  ABB28_RS14275 isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  358.1   0.3  3.5e-111  3.5e-111       2     254 ..       8     247 ..       7     248 .. 0.97
   2 !  272.7   2.0   2.7e-85   2.7e-85     353     527 .]     248     424 ..     247     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 358.1 bits;  conditional E-value: 3.5e-111
                                 TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpv 70 
                                               e+iq++Wdt++rw++i+r+y+a dvv+lrG+v+ e+ l++++a+klw  l+++      +++lGal+++
  lcl|NCBI__GCF_001431535.1:WP_057509262.1   8 EQIQHDWDTNPRWHGIERNYTAADVVRLRGTVHVEHSLARMGAEKLWTYLQEK----DFVNALGALTGN 72 
                                               789*********************************************99754....479********* PP

                                 TIGR01346  71 qvsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakd 138
                                               q++qq+ka l+a+ylsGWqv++danl+++++Pd+++yPad+vP++v+r++++ll++d+  + ++   kd
  lcl|NCBI__GCF_001431535.1:WP_057509262.1  73 QAMQQVKAgLNAIYLSGWQVAADANLAGQMYPDQSLYPADSVPAVVKRINNTLLRADQLHHAEG---KD 138
                                               **********************************************************988765...45 PP

                                 TIGR01346 139 eeelkelyidylvPivadadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqe 207
                                               e       id+l+Pivada+aGfGGvl++f+l+k++ie+Gaagvh+edql+s+kkCGh++Gkvlvp++e
  lcl|NCBI__GCF_001431535.1:WP_057509262.1 139 E-------IDFLQPIVADAEAGFGGVLNAFELMKAMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTRE 200
                                               5.......9************************************************************ PP

                                 TIGR01346 208 hvnrlvaarlaadvmgvetllvartdaeaatlitsdvdardhefivG 254
                                               ++++l+aarlaadv gv+tllvartdaeaa+l+tsd+da d++f +G
  lcl|NCBI__GCF_001431535.1:WP_057509262.1 201 AIEKLNAARLAADVLGVPTLLVARTDAEAADLLTSDIDANDQPFATG 247
                                               ********************************************999 PP

  == domain 2  score: 272.7 bits;  conditional E-value: 2.7e-85
                                 TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnW 421
                                               ert+eGfy++++g+++ai+r+ a+aPyadlvW+et++Pdle a++fae++++kfP+kllayn+sPsfnW
  lcl|NCBI__GCF_001431535.1:WP_057509262.1 248 ERTTEGFYKTRNGLDQAISRGLAYAPYADLVWCETGKPDLEFARQFAEAIHAKFPGKLLAYNCSPSFNW 316
                                               8******************************************************************** PP

                                 TIGR01346 422 dkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvqqrel...edGv 487
                                               +k+l+d +i++f+ e+++ Gy fqfitlaG+h+ ++++f+la+++a++ m a+ve +q+ e+   ++G+
  lcl|NCBI__GCF_001431535.1:WP_057509262.1 317 KKNLDDATIATFQTEIAKYGYRFQFITLAGFHALNYSMFNLAHGYARRQMSAFVE-LQEAEFaaaDRGF 384
                                               *******************************************************.*******999*** PP

                                 TIGR01346 488 dvlkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                               +++khq+e+G++yfd +++ +q G s+t+al++s+ee qf
  lcl|NCBI__GCF_001431535.1:WP_057509262.1 385 TAVKHQREVGTGYFDAVTQAIQQGQSSTTALTGSTEEAQF 424
                                               ***************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (430 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: 00:00:00.04
# Mc/sec: 4.78
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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