Alignments for a candidate for aceA in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Acidovorax sp. GW101-3H11

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate Ac3H11_2831 Isocitrate lyase (EC 4.1.3.1)

Query= reanno::acidovorax_3H11:Ac3H11_2831
         (443 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2831
          Length = 443

 Score =  900 bits (2326), Expect = 0.0
 Identities = 443/443 (100%), Positives = 443/443 (100%)

Query: 1   MPQSLNEQLSREQQIAALEKDWATNPRWKGVKRGYSAADVVRLRGSLPIEHTLAKRGAEK 60
           MPQSLNEQLSREQQIAALEKDWATNPRWKGVKRGYSAADVVRLRGSLPIEHTLAKRGAEK
Sbjct: 1   MPQSLNEQLSREQQIAALEKDWATNPRWKGVKRGYSAADVVRLRGSLPIEHTLAKRGAEK 60

Query: 61  LWDKINGGAKKGYVNAFGAISAGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLY 120
           LWDKINGGAKKGYVNAFGAISAGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLY
Sbjct: 61  LWDKINGGAKKGYVNAFGAISAGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLY 120

Query: 121 AYDSVPTMVRRINNTFKRADEIQWGRGINPGDKEFIDYFLPIVADAEAGFGGVLNAFELM 180
           AYDSVPTMVRRINNTFKRADEIQWGRGINPGDKEFIDYFLPIVADAEAGFGGVLNAFELM
Sbjct: 121 AYDSVPTMVRRINNTFKRADEIQWGRGINPGDKEFIDYFLPIVADAEAGFGGVLNAFELM 180

Query: 181 KNMIQSGAAGVHFEDQLAAVKKCGHMGGKVLVPTQEACEKLISARFAADVMGVSTIVLAR 240
           KNMIQSGAAGVHFEDQLAAVKKCGHMGGKVLVPTQEACEKLISARFAADVMGVSTIVLAR
Sbjct: 181 KNMIQSGAAGVHFEDQLAAVKKCGHMGGKVLVPTQEACEKLISARFAADVMGVSTIVLAR 240

Query: 241 TDAEAANLITSDHDANDKPFLTGERTQEGFYRVKNGLEQAISRGVAYAPYADLVWCETGV 300
           TDAEAANLITSDHDANDKPFLTGERTQEGFYRVKNGLEQAISRGVAYAPYADLVWCETGV
Sbjct: 241 TDAEAANLITSDHDANDKPFLTGERTQEGFYRVKNGLEQAISRGVAYAPYADLVWCETGV 300

Query: 301 PDIGFAREFAQAVHAACPGKLLSYNCSPSFNWKKNLNDKQIASFQEDLSALGYKYQFITL 360
           PDIGFAREFAQAVHAACPGKLLSYNCSPSFNWKKNLNDKQIASFQEDLSALGYKYQFITL
Sbjct: 301 PDIGFAREFAQAVHAACPGKLLSYNCSPSFNWKKNLNDKQIASFQEDLSALGYKYQFITL 360

Query: 361 AGIHINWFNTFQFAHAYANGEGMKHYVNMVQEPEFAARDKGYTFVSHQQEVGAGYFDDVT 420
           AGIHINWFNTFQFAHAYANGEGMKHYVNMVQEPEFAARDKGYTFVSHQQEVGAGYFDDVT
Sbjct: 361 AGIHINWFNTFQFAHAYANGEGMKHYVNMVQEPEFAARDKGYTFVSHQQEVGAGYFDDVT 420

Query: 421 TVIQGGSSSVKALTGSTEEEQFH 443
           TVIQGGSSSVKALTGSTEEEQFH
Sbjct: 421 TVIQGGSSSVKALTGSTEEEQFH 443


Lambda     K      H
   0.317    0.132    0.397 

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: 873
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: 443
Length of database: 443
Length adjustment: 32
Effective length of query: 411
Effective length of database: 411
Effective search space:   168921
Effective search space used:   168921
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 Ac3H11_2831 (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.4517.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   1.9e-194  632.9   3.9   3.9e-111  357.9   0.1    2.0  2  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2831  Isocitrate lyase (EC 4.1.3.1)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2831  Isocitrate lyase (EC 4.1.3.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  357.9   0.1  3.9e-111  3.9e-111       2     254 ..      16     263 ..      15     264 .. 0.98
   2 !  276.8   0.8   1.5e-86   1.5e-86     353     527 .]     264     442 ..     263     442 .. 0.99

  Alignments for each domain:
  == domain 1  score: 357.9 bits;  conditional E-value: 3.9e-111
                                        TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvskt 63 
                                                      + ++k+W t++rw+++kr ysa dvv+lrGs++ e++l++++a+klw+ ++   k k+++++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2831  16 AALEKDWATNPRWKGVKRGYSAADVVRLRGSLPIEHTLAKRGAEKLWDKINGGAK-KGYVNA 76 
                                                      5689**********************************************99887.6***** PP

                                        TIGR01346  64 lGaldpvqvsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallf 124
                                                      +Ga+ ++q++qqaka l+avylsGWqv++d n+s+ ++Pd+++y +d+vP+ v+r+++++++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2831  77 FGAISAGQAMQQAKAgLEAVYLSGWQVAADGNTSETMYPDQSLYAYDSVPTMVRRINNTFKR 138
                                                      ************************************************************** PP

                                        TIGR01346 125 hdrkqkearskakdeeelkelyidylvPivadadaGfGGvlavfkltkllierGaagvhled 186
                                                      +d++q+  ++++ d+      +idy++Pivada+aGfGGvl++f+l+k +i+ Gaagvh+ed
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2831 139 ADEIQWGRGINPGDK-----EFIDYFLPIVADAEAGFGGVLNAFELMKNMIQSGAAGVHFED 195
                                                      *************99.....49**************************************** PP

                                        TIGR01346 187 qlssekkCGhlaGkvlvpvqehvnrlvaarlaadvmgvetllvartdaeaatlitsdvdard 248
                                                      ql+++kkCGh++Gkvlvp+qe+ ++l++ar+aadvmgv t+++artdaeaa+litsd da d
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2831 196 QLAAVKKCGHMGGKVLVPTQEACEKLISARFAADVMGVSTIVLARTDAEAANLITSDHDAND 257
                                                      ************************************************************** PP

                                        TIGR01346 249 hefivG 254
                                                      ++f++G
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2831 258 KPFLTG 263
                                                      *****9 PP

  == domain 2  score: 276.8 bits;  conditional E-value: 1.5e-86
                                        TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllayn 414
                                                      ert+eGfyrvk+g+e+ai+r+ a+aPyadlvW+et+ Pd+  a+efa++v++  P+kll+yn
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2831 264 ERTQEGFYRVKNGLEQAISRGVAYAPYADLVWCETGVPDIGFAREFAQAVHAACPGKLLSYN 325
                                                      8************************************************************* PP

                                        TIGR01346 415 lsPsfnWdkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfak.eGmkayv 475
                                                      +sPsfnW+k+l+d++i++f+++l++lGyk+qfitlaG+h ++++ f++a+++a+ eGmk+yv
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2831 326 CSPSFNWKKNLNDKQIASFQEDLSALGYKYQFITLAGIHINWFNTFQFAHAYANgEGMKHYV 387
                                                      ******************************************************9******* PP

                                        TIGR01346 476 ekvqqrel...edGvdvlkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                                      + vq++e+   ++G+++++hq+e+Ga+yfd++++++qgG s++ al++s+ee+qf
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2831 388 NMVQEPEFaarDKGYTFVSHQQEVGAGYFDDVTTVIQGGSSSVKALTGSTEEEQF 442
                                                      *********999******************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (443 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: 3.78
//
[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