Alignments for a candidate for aceA in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Pseudomonas fluorescens FW300-N2C3

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate AO356_22080 AO356_22080 isocitrate lyase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_22080
          Length = 441

 Score =  885 bits (2287), Expect = 0.0
 Identities = 435/441 (98%), Positives = 438/441 (99%)

Query: 1   MALTREQQIAALEKDWAENPRWKGVTRNYSAADVVRLRGSVQPEHTFAKMGADKLWNLVT 60
           MALTREQQIAALEKDWAENPRWKGV RNYSAADVVRLRGSVQPEHTFAKMGA+KLWNLVT
Sbjct: 1   MALTREQQIAALEKDWAENPRWKGVKRNYSAADVVRLRGSVQPEHTFAKMGAEKLWNLVT 60

Query: 61  QGAKPSFRPEKDFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLY 120
           QGAKP+FRPEKDFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLY
Sbjct: 61  QGAKPAFRPEKDFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLY 120

Query: 121 PVDSVPTVVKRINNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELM 180
           PVDSVPTVVKRINNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELM
Sbjct: 121 PVDSVPTVVKRINNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELM 180

Query: 181 KSMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGTPTIILAR 240
           KSMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAG PTIILAR
Sbjct: 181 KSMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGVPTIILAR 240

Query: 241 TDANAADLLTSDCDPYDQPFVTGERTQEGFYKVRAGLDQAIARGLAYAPFADLIWCETAK 300
           TDANAADLLTSDCDPYDQPFVTG RTQEGFYKVRAGLDQAIARGLAYAP+ADLIWCETAK
Sbjct: 241 TDANAADLLTSDCDPYDQPFVTGTRTQEGFYKVRAGLDQAIARGLAYAPYADLIWCETAK 300

Query: 301 PDLDEARRFAEAIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITL 360
           PDLDEARRFAEAIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITL
Sbjct: 301 PDLDEARRFAEAIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITL 360

Query: 361 AGIHNMWHSMFNLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTV 420
           AGIHNMWHSMFNLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTV
Sbjct: 361 AGIHNMWHSMFNLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTV 420

Query: 421 IQGGTSSVTALTGSTEEEQFH 441
           IQGGTSSVTALTGSTEEEQFH
Sbjct: 421 IQGGTSSVTALTGSTEEEQFH 441


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: 892
Number of extensions: 12
Number of successful extensions: 1
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: 441
Length adjustment: 32
Effective length of query: 409
Effective length of database: 409
Effective search space:   167281
Effective search space used:   167281
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 AO356_22080 AO356_22080 (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.19947.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
     2e-200  652.6   5.2   1.2e-115  372.9   0.1    2.0  2  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080  AO356_22080 isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080  AO356_22080 isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.9   0.1  1.2e-115  1.2e-115       2     254 ..      10     263 ..       9     265 .. 0.97
   2 !  282.2   1.7   3.5e-88   3.5e-88     354     527 .]     265     440 ..     264     440 .. 0.99

  Alignments for each domain:
  == domain 1  score: 372.9 bits;  conditional E-value: 1.2e-115
                                       TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkesk.....ekt 59 
                                                     + ++k+W  ++rw+++kr+ysa dvv+lrGsv++e++ ++++a+klw+++++  k     ek 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080  10 AALEKDWAENPRWKGVKRNYSAADVVRLRGSVQPEHTFAKMGAEKLWNLVTQGAKpafrpEKD 72 
                                                     5689**********************************************9986544444799 PP

                                       TIGR01346  60 vsktlGaldpvqvsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfka 121
                                                      ++++Gal+++q++qq+ka ++a+ylsGWqv++d+n +++++Pd+++yP+d+vP++v+r++++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080  73 FVNCMGALTGGQAVQQVKAgIQAIYLSGWQVAADNNSAESMYPDQSLYPVDSVPTVVKRINNS 135
                                                     *************************************************************** PP

                                       TIGR01346 122 llfhdrkqkearskakdeeelkelyidylvPivadadaGfGGvlavfkltkllierGaagvhl 184
                                                     ++++d++q++a++++ de      yidy+ Pivada+aGfGGvl++++l+k +ie+Gaagvh+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080 136 FRRADQIQWKAGKNPGDE-----GYIDYFAPIVADAEAGFGGVLNAYELMKSMIEAGAAGVHF 193
                                                     ***************999.....7*************************************** PP

                                       TIGR01346 185 edqlssekkCGhlaGkvlvpvqehvnrlvaarlaadvmgvetllvartdaeaatlitsdvdar 247
                                                     edql+s+kkCGh++Gkvlvp+qe+v++l aarlaadv+gv+t+++artda+aa+l+tsd+d++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080 194 EDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGVPTIILARTDANAADLLTSDCDPY 256
                                                     *************************************************************** PP

                                       TIGR01346 248 dhefivG 254
                                                     d++f++G
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080 257 DQPFVTG 263
                                                     ******9 PP

  == domain 2  score: 282.2 bits;  conditional E-value: 3.5e-88
                                       TIGR01346 354 rtreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynls 416
                                                     rt+eGfy+v++g+++ai+r+ a+aPyadl+W+et++Pdl+ea++fae++k+++Pd+ll+yn+s
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080 265 RTQEGFYKVRAGLDQAIARGLAYAPYADLIWCETAKPDLDEARRFAEAIKKEYPDQLLSYNCS 327
                                                     9************************************************************** PP

                                       TIGR01346 417 PsfnWdkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvq 479
                                                     PsfnW+k+l+d +i+kf++el+++Gyk+qfitlaG+h ++ ++f+la+d+a++ m+ayv+ +q
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080 328 PSFNWKKNLDDATIAKFQRELSAMGYKHQFITLAGIHNMWHSMFNLAHDYARNDMTAYVK-LQ 389
                                                     ***********************************************************8.** PP

                                       TIGR01346 480 qrel...edGvdvlkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                                     ++e+    +G+++++hq+e+G++yfd++++++qgG+s+++al++s+ee+qf
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080 390 EQEFadaAKGYTFVAHQQEVGTGYFDDMTTVIQGGTSSVTALTGSTEEEQF 440
                                                     ****98889*****************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (441 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: 4.89
//
[ok]

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

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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