Alignments for a candidate for aceA in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Pseudomonas putida KT2440

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate PP_4116 PP_4116 isocitrate lyase

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



>FitnessBrowser__Putida:PP_4116
          Length = 441

 Score =  862 bits (2227), Expect = 0.0
 Identities = 419/441 (95%), Positives = 432/441 (97%)

Query: 1   MALTREQQIAALEKDWAENPRWKGVTRNYSAADVVRLRGSVQPEHTFAKMGADKLWNLVT 60
           MALTREQQIAALEKDWAENPRWKGVTR Y+AADVVRLRGSVQPEHTFA+ GA+KLW LVT
Sbjct: 1   MALTREQQIAALEKDWAENPRWKGVTRTYTAADVVRLRGSVQPEHTFARQGAEKLWKLVT 60

Query: 61  QGAKPSFRPEKDFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLY 120
           +GA PSFRP+KDFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLY
Sbjct: 61  EGAHPSFRPDKDFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLY 120

Query: 121 PVDSVPTVVKRINNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELM 180
           PVDSVPTVVKRINN+FRRADQIQWKAGKNPGD+GYIDYFAPIVADAEAGFGGVLNAYELM
Sbjct: 121 PVDSVPTVVKRINNAFRRADQIQWKAGKNPGDDGYIDYFAPIVADAEAGFGGVLNAYELM 180

Query: 181 KSMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGTPTIILAR 240
           K+MIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKL AARLAADV+G PTIILAR
Sbjct: 181 KNMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVAARLAADVSGVPTIILAR 240

Query: 241 TDANAADLLTSDCDPYDQPFVTGERTQEGFYKVRAGLDQAIARGLAYAPFADLIWCETAK 300
           TDANAADLLTSDCDPYDQPFV GERT+EGFYKVRAGLDQAIARGLAYAP+ADLIWCETAK
Sbjct: 241 TDANAADLLTSDCDPYDQPFVVGERTREGFYKVRAGLDQAIARGLAYAPYADLIWCETAK 300

Query: 301 PDLDEARRFAEAIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITL 360
           PDLDEARRFAEAIKKEYPDQ+LSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITL
Sbjct: 301 PDLDEARRFAEAIKKEYPDQILSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITL 360

Query: 361 AGIHNMWHSMFNLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTV 420
           AGIHNMWH MFNLAHDYARNDMTAYVKLQEQEFADA+KGYTFVAHQQEVGTGYFDDMTTV
Sbjct: 361 AGIHNMWHGMFNLAHDYARNDMTAYVKLQEQEFADASKGYTFVAHQQEVGTGYFDDMTTV 420

Query: 421 IQGGTSSVTALTGSTEEEQFH 441
           IQGG SSVTALTGSTEEEQFH
Sbjct: 421 IQGGASSVTALTGSTEEEQFH 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: 877
Number of extensions: 17
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 PP_4116 PP_4116 (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.19258.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.9e-201  654.1   4.7   1.3e-115  372.7   0.1    2.0  2  lcl|FitnessBrowser__Putida:PP_4116  PP_4116 isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4116  PP_4116 isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.7   0.1  1.3e-115  1.3e-115       2     254 ..      10     263 ..       9     264 .. 0.96
   2 !  283.4   1.2   1.5e-88   1.5e-88     353     527 .]     264     440 ..     264     440 .. 0.99

  Alignments for each domain:
  == domain 1  score: 372.7 bits;  conditional E-value: 1.3e-115
                           TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkesk.....ektvsktlGaldpvq 71 
                                         + ++k+W  ++rw++++r y+a dvv+lrGsv++e++ ++++a+klw+++++  +     +k  ++++Gal+++q
  lcl|FitnessBrowser__Putida:PP_4116  10 AALEKDWAENPRWKGVTRTYTAADVVRLRGSVQPEHTFARQGAEKLWKLVTEGAHpsfrpDKDFVNCMGALTGGQ 84 
                                         5689**********************************************9754322333789************ PP

                           TIGR01346  72 vsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakdeeelkel 145
                                         ++qq+ka ++a+ylsGWqv++d+n +++++Pd+++yP+d+vP++v+r+++a++++d++q++a++++ d+      
  lcl|FitnessBrowser__Putida:PP_4116  85 AVQQVKAgIQAIYLSGWQVAADNNSAESMYPDQSLYPVDSVPTVVKRINNAFRRADQIQWKAGKNPGDD-----G 154
                                         ******************************************************************999.....7 PP

                           TIGR01346 146 yidylvPivadadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqehvnrlvaarlaad 220
                                         yidy+ Pivada+aGfGGvl++++l+k +ie+Gaagvh+edql+s+kkCGh++Gkvlvp+qe+v++lvaarlaad
  lcl|FitnessBrowser__Putida:PP_4116 155 YIDYFAPIVADAEAGFGGVLNAYELMKNMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVAARLAAD 229
                                         *************************************************************************** PP

                           TIGR01346 221 vmgvetllvartdaeaatlitsdvdardhefivG 254
                                         v gv+t+++artda+aa+l+tsd+d++d++f+vG
  lcl|FitnessBrowser__Putida:PP_4116 230 VSGVPTIILARTDANAADLLTSDCDPYDQPFVVG 263
                                         *********************************9 PP

  == domain 2  score: 283.4 bits;  conditional E-value: 1.5e-88
                           TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnWdkaled 427
                                         ertreGfy+v++g+++ai+r+ a+aPyadl+W+et++Pdl+ea++fae++k+++Pd++l+yn+sPsfnW+k+l+d
  lcl|FitnessBrowser__Putida:PP_4116 264 ERTREGFYKVRAGLDQAIARGLAYAPYADLIWCETAKPDLDEARRFAEAIKKEYPDQILSYNCSPSFNWKKNLDD 338
                                         7************************************************************************** PP

                           TIGR01346 428 deikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvqqrel...edGvdvlkhqkesGae 499
                                          +i+kf++el+++Gyk+qfitlaG+h ++ ++f+la+d+a++ m+ayv+ +q++e+   ++G+++++hq+e+G++
  lcl|FitnessBrowser__Putida:PP_4116 339 ATIAKFQRELSAMGYKHQFITLAGIHNMWHGMFNLAHDYARNDMTAYVK-LQEQEFadaSKGYTFVAHQQEVGTG 412
                                         ************************************************8.******98889************** PP

                           TIGR01346 500 yfdqllklvqgGvsataalaksveedqf 527
                                         yfd++++++qgG s+++al++s+ee+qf
  lcl|FitnessBrowser__Putida:PP_4116 413 YFDDMTTVIQGGASSVTALTGSTEEEQF 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: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 3.99
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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