Alignments for a candidate for aceA in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Shewanella oneidensis MR-1

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate 200655 SO1484 isocitrate lyase (NCBI ptt file)

Query= reanno::MR1:200655
         (440 letters)



>FitnessBrowser__MR1:200655
          Length = 440

 Score =  887 bits (2292), Expect = 0.0
 Identities = 440/440 (100%), Positives = 440/440 (100%)

Query: 1   MTKATQTSRQAQIDAIKKDWAENPRWKNVRRPYTAEEVVALRGSIVPENTIAKRGAAKLW 60
           MTKATQTSRQAQIDAIKKDWAENPRWKNVRRPYTAEEVVALRGSIVPENTIAKRGAAKLW
Sbjct: 1   MTKATQTSRQAQIDAIKKDWAENPRWKNVRRPYTAEEVVALRGSIVPENTIAKRGAAKLW 60

Query: 61  DLVNGGSKKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGTMYPDQSLYPA 120
           DLVNGGSKKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGTMYPDQSLYPA
Sbjct: 61  DLVNGGSKKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGTMYPDQSLYPA 120

Query: 121 NSVPAVVSRINNSFRRADQIQWSNGVNPEDENFVDYFLPIIADAEAGFGGVLNAFELMKS 180
           NSVPAVVSRINNSFRRADQIQWSNGVNPEDENFVDYFLPIIADAEAGFGGVLNAFELMKS
Sbjct: 121 NSVPAVVSRINNSFRRADQIQWSNGVNPEDENFVDYFLPIIADAEAGFGGVLNAFELMKS 180

Query: 181 MIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVAARLAADVSGVETLVIARTD 240
           MIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVAARLAADVSGVETLVIARTD
Sbjct: 181 MIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVAARLAADVSGVETLVIARTD 240

Query: 241 ANAADLLTSDCDPYDRDFVTGERTNEGFYRVNAGLDQAISRGLAYAPYADLIWCETAKPD 300
           ANAADLLTSDCDPYDRDFVTGERTNEGFYRVNAGLDQAISRGLAYAPYADLIWCETAKPD
Sbjct: 241 ANAADLLTSDCDPYDRDFVTGERTNEGFYRVNAGLDQAISRGLAYAPYADLIWCETAKPD 300

Query: 301 LEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQALSDMGYKYQFITLAG 360
           LEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQALSDMGYKYQFITLAG
Sbjct: 301 LEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQALSDMGYKYQFITLAG 360

Query: 361 IHNMWYNMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVGTGYFDQVTTV 420
           IHNMWYNMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVGTGYFDQVTTV
Sbjct: 361 IHNMWYNMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVGTGYFDQVTTV 420

Query: 421 IQGGHSSVTALTGSTEEEQF 440
           IQGGHSSVTALTGSTEEEQF
Sbjct: 421 IQGGHSSVTALTGSTEEEQF 440


Lambda     K      H
   0.317    0.132    0.390 

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: 884
Number of extensions: 29
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: 440
Length of database: 440
Length adjustment: 32
Effective length of query: 408
Effective length of database: 408
Effective search space:   166464
Effective search space used:   166464
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 200655 SO1484 (isocitrate lyase (NCBI ptt file))
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.1879.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.7e-208  678.1   6.0   1.9e-118  382.0   0.1    2.0  2  lcl|FitnessBrowser__MR1:200655  SO1484 isocitrate lyase (NCBI pt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200655  SO1484 isocitrate lyase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.0   0.1  1.9e-118  1.9e-118       2     254 ..      14     261 ..      13     263 .. 0.98
   2 !  299.1   2.0   2.6e-93   2.6e-93     353     527 .]     262     440 .]     261     440 .] 0.99

  Alignments for each domain:
  == domain 1  score: 382.0 bits;  conditional E-value: 1.9e-118
                       TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpvqvsqqaka.l 79 
                                     + i+k+W  ++rw++++r+y+a++vv lrGs+ +e+++++++a+klw++++  sk k+++++lGal+++q++qqaka +
  lcl|FitnessBrowser__MR1:200655  14 DAIKKDWAENPRWKNVRRPYTAEEVVALRGSIVPENTIAKRGAAKLWDLVNGGSK-KGYVNSLGALTGGQAVQQAKAgI 91 
                                     5799***********************************************9998.6********************** PP

                       TIGR01346  80 davylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakdeeelkelyidylvPivadad 158
                                     +a+ylsGWqv++danl++ ++Pd+++yPa++vP++v r++++++++d++q++++ +++de      ++dy++Pi+ada+
  lcl|FitnessBrowser__MR1:200655  92 EAIYLSGWQVAADANLAGTMYPDQSLYPANSVPAVVSRINNSFRRADQIQWSNGVNPEDE-----NFVDYFLPIIADAE 165
                                     *******************************************************99998.....69************ PP

                       TIGR01346 159 aGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqehvnrlvaarlaadvmgvetllvartdaeaa 237
                                     aGfGGvl++f+l+k +i++Gaagvh+edql+s+kkCGh++Gkvlvp+qe+v++lvaarlaadv gvetl++artda+aa
  lcl|FitnessBrowser__MR1:200655 166 AGFGGVLNAFELMKSMIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVAARLAADVSGVETLVIARTDANAA 244
                                     ******************************************************************************* PP

                       TIGR01346 238 tlitsdvdardhefivG 254
                                     +l+tsd+d++d++f++G
  lcl|FitnessBrowser__MR1:200655 245 DLLTSDCDPYDRDFVTG 261
                                     ****************9 PP

  == domain 2  score: 299.1 bits;  conditional E-value: 2.6e-93
                       TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnWdkaleddeik 431
                                     ert+eGfyrv++g+++ai+r+ a+aPyadl+W+et++Pdleea++fae++++++Pd+llayn+sPsfnW+k+l+d +i+
  lcl|FitnessBrowser__MR1:200655 262 ERTNEGFYRVNAGLDQAISRGLAYAPYADLIWCETAKPDLEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIA 340
                                     8****************************************************************************** PP

                       TIGR01346 432 kfikelgdlGykfqfitlaGlhsealavfdlakdfak.eGmkayvekvqqrel...edGvdvlkhqkesGaeyfdqllk 506
                                     +f++ l+d+Gyk+qfitlaG+h +++++fdla+d+a+ eGmk+yvekvq+ e+   ++G+++++hq+e+G++yfdq+++
  lcl|FitnessBrowser__MR1:200655 341 RFQQALSDMGYKYQFITLAGIHNMWYNMFDLAYDYARgEGMKHYVEKVQEVEFaaaKKGYTFVAHQQEVGTGYFDQVTT 419
                                     ******************************************************999********************** PP

                       TIGR01346 507 lvqgGvsataalaksveedqf 527
                                     ++qgG s+++al++s+ee+qf
  lcl|FitnessBrowser__MR1:200655 420 VIQGGHSSVTALTGSTEEEQF 440
                                     ********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (440 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: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 2.88
//
[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