Aligments for a candidate for aceA in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Aligments for a candidate for aceA in Shewanella loihica PV-4

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate 5208774 Shew_1276 isocitrate lyase (RefSeq)

Query= reanno::PV4:5208774
         (450 letters)



>lcl|FitnessBrowser__PV4:5208774 Shew_1276 isocitrate lyase (RefSeq)
          Length = 450

 Score =  907 bits (2344), Expect = 0.0
 Identities = 450/450 (100%), Positives = 450/450 (100%)

Query: 1   MLTPEMEKIMTKATTQISRQQQIDAIKQDWAENPRWAGVRRPYSAEDVVALRGSIVPENT 60
           MLTPEMEKIMTKATTQISRQQQIDAIKQDWAENPRWAGVRRPYSAEDVVALRGSIVPENT
Sbjct: 1   MLTPEMEKIMTKATTQISRQQQIDAIKQDWAENPRWAGVRRPYSAEDVVALRGSIVPENT 60

Query: 61  LATRGAEKLWQLVNGGAKKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGT 120
           LATRGAEKLWQLVNGGAKKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGT
Sbjct: 61  LATRGAEKLWQLVNGGAKKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGT 120

Query: 121 MYPDQSLYPANSVPAVVQRINNSFRRADQIQWSNEIDPQDERYTDYFLPIVADAEAGFGG 180
           MYPDQSLYPANSVPAVVQRINNSFRRADQIQWSNEIDPQDERYTDYFLPIVADAEAGFGG
Sbjct: 121 MYPDQSLYPANSVPAVVQRINNSFRRADQIQWSNEIDPQDERYTDYFLPIVADAEAGFGG 180

Query: 181 VLNAYELMKNMIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVSARLAADVSG 240
           VLNAYELMKNMIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVSARLAADVSG
Sbjct: 181 VLNAYELMKNMIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVSARLAADVSG 240

Query: 241 VPTLVIARTDANAADLLTSDCDPYDRDFITGERTSEGFYRVNAGIDQAISRGLAYAPYAD 300
           VPTLVIARTDANAADLLTSDCDPYDRDFITGERTSEGFYRVNAGIDQAISRGLAYAPYAD
Sbjct: 241 VPTLVIARTDANAADLLTSDCDPYDRDFITGERTSEGFYRVNAGIDQAISRGLAYAPYAD 300

Query: 301 LIWCETAKPDLEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQELSDMG 360
           LIWCETAKPDLEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQELSDMG
Sbjct: 301 LIWCETAKPDLEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQELSDMG 360

Query: 361 YKYQFITLAGIHNMWYNMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVG 420
           YKYQFITLAGIHNMWYNMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVG
Sbjct: 361 YKYQFITLAGIHNMWYNMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVG 420

Query: 421 TGYFDKVTNVIQGGESSVTALTGSTEEEQF 450
           TGYFDKVTNVIQGGESSVTALTGSTEEEQF
Sbjct: 421 TGYFDKVTNVIQGGESSVTALTGSTEEEQF 450


Lambda     K      H
   0.316    0.132    0.389 

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: 900
Number of extensions: 21
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: 450
Length of database: 450
Length adjustment: 33
Effective length of query: 417
Effective length of database: 417
Effective search space:   173889
Effective search space used:   173889
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 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate 5208774 Shew_1276 (isocitrate lyase (RefSeq))
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.8771.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   6.4e-209  680.6   5.7   8.6e-119  383.2   0.1    2.0  2  lcl|FitnessBrowser__PV4:5208774  Shew_1276 isocitrate lyase (RefS


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208774  Shew_1276 isocitrate lyase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.2   0.1  8.6e-119  8.6e-119       2     254 ..      24     271 ..      23     273 .. 0.98
   2 !  300.6   1.6   9.4e-94   9.4e-94     353     527 .]     272     450 .]     271     450 .] 0.99

  Alignments for each domain:
  == domain 1  score: 383.2 bits;  conditional E-value: 8.6e-119
                        TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpvqvsqqaka. 78 
                                      + i+++W  ++rw +++r+ysa+dvv lrGs+ +e++l+ ++a+klw++++   k k+++++lGal+++q++qqaka 
  lcl|FitnessBrowser__PV4:5208774  24 DAIKQDWAENPRWAGVRRPYSAEDVVALRGSIVPENTLATRGAEKLWQLVNGGAK-KGYVNSLGALTGGQAVQQAKAg 100
                                      5799**********************************************99877.6********************* PP

                        TIGR01346  79 ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakdeeelkelyidylvPivad 156
                                      ++a+ylsGWqv++danl++ ++Pd+++yPa++vP++v+r++++++++d++q+++ ++++de      y dy++Pivad
  lcl|FitnessBrowser__PV4:5208774 101 IEAIYLSGWQVAADANLAGTMYPDQSLYPANSVPAVVQRINNSFRRADQIQWSNEIDPQDE-----RYTDYFLPIVAD 173
                                      ********************************************************99998.....599********* PP

                        TIGR01346 157 adaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqehvnrlvaarlaadvmgvetllvartda 234
                                      a+aGfGGvl++++l+k +i++Gaagvh+edql+s+kkCGh++Gkvlvp+qe+v++lv+arlaadv gv+tl++artda
  lcl|FitnessBrowser__PV4:5208774 174 AEAGFGGVLNAYELMKNMIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVSARLAADVSGVPTLVIARTDA 251
                                      ****************************************************************************** PP

                        TIGR01346 235 eaatlitsdvdardhefivG 254
                                      +aa+l+tsd+d++d++fi+G
  lcl|FitnessBrowser__PV4:5208774 252 NAADLLTSDCDPYDRDFITG 271
                                      *******************9 PP

  == domain 2  score: 300.6 bits;  conditional E-value: 9.4e-94
                        TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnWdkaleddei 430
                                      ert+eGfyrv++g+++ai+r+ a+aPyadl+W+et++Pdleea++fae++++++Pd+llayn+sPsfnW+k+l+d +i
  lcl|FitnessBrowser__PV4:5208774 272 ERTSEGFYRVNAGIDQAISRGLAYAPYADLIWCETAKPDLEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATI 349
                                      8***************************************************************************** PP

                        TIGR01346 431 kkfikelgdlGykfqfitlaGlhsealavfdlakdfak.eGmkayvekvqqrel...edGvdvlkhqkesGaeyfdql 504
                                      ++f++el+d+Gyk+qfitlaG+h +++++fdla+d+a+ eGmk+yvekvq+ e+   ++G+++++hq+e+G++yfd++
  lcl|FitnessBrowser__PV4:5208774 350 ARFQQELSDMGYKYQFITLAGIHNMWYNMFDLAYDYARgEGMKHYVEKVQEVEFaaaKKGYTFVAHQQEVGTGYFDKV 427
                                      *******************************************************999******************** PP

                        TIGR01346 505 lklvqgGvsataalaksveedqf 527
                                      ++++qgG s+++al++s+ee+qf
  lcl|FitnessBrowser__PV4:5208774 428 TNVIQGGESSVTALTGSTEEEQF 450
                                      **********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (450 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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