Alignments for a candidate for aceA in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Pseudomonas fluorescens GW456-L13

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate PfGW456L13_2633 Isocitrate lyase (EC 4.1.3.1)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2633
          Length = 441

 Score =  885 bits (2288), Expect = 0.0
 Identities = 434/441 (98%), Positives = 440/441 (99%)

Query: 1   MALTREQQIAALEKDWAENPRWKGVTRNYSAADVVRLRGSVQPEHTFAKMGADKLWNLVT 60
           MALTREQQIAALEKDWAENPRWKGVTR YSAADVVRLRGSVQPEHTFAKMGA+KLWNLVT
Sbjct: 1   MALTREQQIAALEKDWAENPRWKGVTRTYSAADVVRLRGSVQPEHTFAKMGAEKLWNLVT 60

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

Query: 121 PVDSVPTVVKRINNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELM 180
           PVDSVPTVVKRINNSFRRADQIQWKAGKNPGD+GYIDYFAPIVADAEAGFGGVLNAYELM
Sbjct: 121 PVDSVPTVVKRINNSFRRADQIQWKAGKNPGDDGYIDYFAPIVADAEAGFGGVLNAYELM 180

Query: 181 KSMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGTPTIILAR 240
           KSMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGTPTIILAR
Sbjct: 181 KSMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGTPTIILAR 240

Query: 241 TDANAADLLTSDCDPYDQPFVTGERTQEGFYKVRAGLDQAIARGLAYAPFADLIWCETAK 300
           TDANAADLLTSDCDPYDQPFVTGERTQEGFYKVRAGLDQAIARGLAYAP+ADLIWCETAK
Sbjct: 241 TDANAADLLTSDCDPYDQPFVTGERTQEGFYKVRAGLDQAIARGLAYAPYADLIWCETAK 300

Query: 301 PDLDEARRFAEAIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITL 360
           PDLDEARRFAEAIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITL
Sbjct: 301 PDLDEARRFAEAIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITL 360

Query: 361 AGIHNMWHSMFNLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTV 420
           AGIHNMWHSMFNLAHDYARNDMTAYVKLQEQEFADA+KGYTFVAHQQEVGTGYFDDMTTV
Sbjct: 361 AGIHNMWHSMFNLAHDYARNDMTAYVKLQEQEFADASKGYTFVAHQQEVGTGYFDDMTTV 420

Query: 421 IQGGTSSVTALTGSTEEEQFH 441
           IQGG+SSVTALTGSTEEEQFH
Sbjct: 421 IQGGSSSVTALTGSTEEEQFH 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: 885
Number of extensions: 11
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 PfGW456L13_2633 (Isocitrate lyase (EC 4.1.3.1))
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.12622.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   1.8e-199  649.5   5.2   1.7e-114  369.1   0.1    2.0  2  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2633  Isocitrate lyase (EC 4.1.3.1)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2633  Isocitrate lyase (EC 4.1.3.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.1   0.1  1.7e-114  1.7e-114       2     254 ..      10     263 ..       9     264 .. 0.97
   2 !  282.7   1.4   2.5e-88   2.5e-88     353     527 .]     264     440 ..     264     440 .. 0.99

  Alignments for each domain:
  == domain 1  score: 369.1 bits;  conditional E-value: 1.7e-114
                                               TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkesk 56 
                                                             + ++k+W  ++rw++++r ysa dvv+lrGsv++e++ ++++a+klw+++++  k
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2633  10 AALEKDWAENPRWKGVTRTYSAADVVRLRGSVQPEHTFAKMGAEKLWNLVTQGAK 64 
                                                             5689**********************************************99865 PP

                                               TIGR01346  57 .....ektvsktlGaldpvqvsqqaka.ldavylsGWqvssdanlsnepgPdlad 105
                                                                  ek  ++++Gal+++q++qq+ka ++a+ylsGWqv++d+n +++++Pd+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2633  65 pafrpEKDFVNCMGALTGGQAVQQVKAgIQAIYLSGWQVAADNNSAESMYPDQSL 119
                                                             44444799*********************************************** PP

                                               TIGR01346 106 yPadtvPnkverlfkallfhdrkqkearskakdeeelkelyidylvPivadadaG 160
                                                             yP+d+vP++v+r++++++++d++q++a++++ d+      yidy+ Pivada+aG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2633 120 YPVDSVPTVVKRINNSFRRADQIQWKAGKNPGDD-----GYIDYFAPIVADAEAG 169
                                                             *******************************999.....7*************** PP

                                               TIGR01346 161 fGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqehvnrlvaa 215
                                                             fGGvl++++l+k +ie+Gaagvh+edql+s+kkCGh++Gkvlvp+qe+v++l aa
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2633 170 FGGVLNAYELMKSMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAA 224
                                                             ******************************************************* PP

                                               TIGR01346 216 rlaadvmgvetllvartdaeaatlitsdvdardhefivG 254
                                                             rlaadv+g++t+++artda+aa+l+tsd+d++d++f++G
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2633 225 RLAADVAGTPTIILARTDANAADLLTSDCDPYDQPFVTG 263
                                                             **************************************9 PP

  == domain 2  score: 282.7 bits;  conditional E-value: 2.5e-88
                                               TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfP 407
                                                             ert+eGfy+v++g+++ai+r+ a+aPyadl+W+et++Pdl+ea++fae++k+++P
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2633 264 ERTQEGFYKVRAGLDQAIARGLAYAPYADLIWCETAKPDLDEARRFAEAIKKEYP 318
                                                             7****************************************************** PP

                                               TIGR01346 408 dkllaynlsPsfnWdkaleddeikkfikelgdlGykfqfitlaGlhsealavfdl 462
                                                             d+ll+yn+sPsfnW+k+l+d +i+kf++el+++Gyk+qfitlaG+h ++ ++f+l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2633 319 DQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITLAGIHNMWHSMFNL 373
                                                             ******************************************************* PP

                                               TIGR01346 463 akdfakeGmkayvekvqqrel...edGvdvlkhqkesGaeyfdqllklvqgGvsa 514
                                                             a+d+a++ m+ayv+ +q++e+   ++G+++++hq+e+G++yfd++++++qgG s+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2633 374 AHDYARNDMTAYVK-LQEQEFadaSKGYTFVAHQQEVGTGYFDDMTTVIQGGSSS 427
                                                             *************8.******98889***************************** PP

                                               TIGR01346 515 taalaksveedqf 527
                                                             ++al++s+ee+qf
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2633 428 VTALTGSTEEEQF 440
                                                             ************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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 3.42
//
[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