Alignments for a candidate for aceA in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Dechlorosoma suillum PS

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate Dsui_0011 Dsui_0011 isocitrate lyase

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



>FitnessBrowser__PS:Dsui_0011
          Length = 436

 Score =  820 bits (2118), Expect = 0.0
 Identities = 399/434 (91%), Positives = 418/434 (96%)

Query: 10  SREQQIAALEKDWATNPRWKGVKRGYSAADVVRLRGSLPIEHTLAKRGAEKLWDKINGGA 69
           +REQQIAALEKDWA NPRWKGVKRGYSAADVVRLRGSL  E+T A+RGA+ LW+K+NGGA
Sbjct: 3   TREQQIAALEKDWAENPRWKGVKRGYSAADVVRLRGSLQPEYTFAQRGAKVLWEKVNGGA 62

Query: 70  KKGYVNAFGAISAGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLYAYDSVPTMV 129
           KKGYVNAFGAI+AGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLYAYDSVPTMV
Sbjct: 63  KKGYVNAFGAITAGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLYAYDSVPTMV 122

Query: 130 RRINNTFKRADEIQWGRGINPGDKEFIDYFLPIVADAEAGFGGVLNAFELMKNMIQSGAA 189
           RRINNTFKRADEIQW RGINPGDKEFIDYFLPIVADAEAGFGGVLNAFELMKNMI +GAA
Sbjct: 123 RRINNTFKRADEIQWSRGINPGDKEFIDYFLPIVADAEAGFGGVLNAFELMKNMIAAGAA 182

Query: 190 GVHFEDQLAAVKKCGHMGGKVLVPTQEACEKLISARFAADVMGVSTIVLARTDAEAANLI 249
           GVHFEDQLAA KKCGHMGGKVLVPT+EA EKLISARFAADVMGV T++LARTDAEAANLI
Sbjct: 183 GVHFEDQLAAAKKCGHMGGKVLVPTREAVEKLISARFAADVMGVPTLILARTDAEAANLI 242

Query: 250 TSDHDANDKPFLTGERTQEGFYRVKNGLEQAISRGVAYAPYADLVWCETGVPDIGFAREF 309
           TSD+DANDKPFLTGERTQEGF+RVKNGLEQ+ISRGVAYAPYADLVWCETGVPDIGFAREF
Sbjct: 243 TSDYDANDKPFLTGERTQEGFFRVKNGLEQSISRGVAYAPYADLVWCETGVPDIGFAREF 302

Query: 310 AQAVHAACPGKLLSYNCSPSFNWKKNLNDKQIASFQEDLSALGYKYQFITLAGIHINWFN 369
           AQAVHAACPGKLLSYNCSPSFNWKKNLND QIASFQE+LSALGYKYQFITLAGIH+NW+N
Sbjct: 303 AQAVHAACPGKLLSYNCSPSFNWKKNLNDSQIASFQEELSALGYKYQFITLAGIHVNWYN 362

Query: 370 TFQFAHAYANGEGMKHYVNMVQEPEFAARDKGYTFVSHQQEVGAGYFDDVTTVIQGGSSS 429
           TF+FA AYA GEGMKHYV MVQEPEFAAR+ GYTFVSHQQEVG GYFDDVTTVIQGGSSS
Sbjct: 363 TFKFAKAYAGGEGMKHYVEMVQEPEFAAREDGYTFVSHQQEVGTGYFDDVTTVIQGGSSS 422

Query: 430 VKALTGSTEEEQFH 443
           VKALTGSTEEEQFH
Sbjct: 423 VKALTGSTEEEQFH 436


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: 831
Number of extensions: 24
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: 436
Length adjustment: 32
Effective length of query: 411
Effective length of database: 404
Effective search space:   166044
Effective search space used:   166044
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 Dsui_0011 Dsui_0011 (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.19979.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.4e-195  635.8   2.7   1.1e-111  359.8   0.1    2.0  2  lcl|FitnessBrowser__PS:Dsui_0011  Dsui_0011 isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0011  Dsui_0011 isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.8   0.1  1.1e-111  1.1e-111       2     254 ..       9     256 ..       8     258 .. 0.98
   2 !  277.3   0.5   1.1e-86   1.1e-86     353     527 .]     257     435 ..     256     435 .. 0.99

  Alignments for each domain:
  == domain 1  score: 359.8 bits;  conditional E-value: 1.1e-111
                         TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpvqvsqqaka 78 
                                       + ++k+W  ++rw+++kr ysa dvv+lrGs+++e + ++++ak lw+ ++   k k++++++Ga++++q++qqaka
  lcl|FitnessBrowser__PS:Dsui_0011   9 AALEKDWAENPRWKGVKRGYSAADVVRLRGSLQPEYTFAQRGAKVLWEKVNGGAK-KGYVNAFGAITAGQAMQQAKA 84 
                                       5689**********************************************99887.6******************** PP

                         TIGR01346  79 .ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakdeeelkelyidylvPiv 154
                                        l+avylsGWqv++d n+s+ ++Pd+++y +d+vP+ v+r++++++++d++q++ ++++ d+      +idy++Piv
  lcl|FitnessBrowser__PS:Dsui_0011  85 gLEAVYLSGWQVAADGNTSETMYPDQSLYAYDSVPTMVRRINNTFKRADEIQWSRGINPGDK-----EFIDYFLPIV 156
                                       ************************************************************99.....49******** PP

                         TIGR01346 155 adadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqehvnrlvaarlaadvmgvetllvar 231
                                       ada+aGfGGvl++f+l+k +i++Gaagvh+edql++ kkCGh++Gkvlvp++e+v++l++ar+aadvmgv+tl++ar
  lcl|FitnessBrowser__PS:Dsui_0011 157 ADAEAGFGGVLNAFELMKNMIAAGAAGVHFEDQLAAAKKCGHMGGKVLVPTREAVEKLISARFAADVMGVPTLILAR 233
                                       ***************************************************************************** PP

                         TIGR01346 232 tdaeaatlitsdvdardhefivG 254
                                       tdaeaa+litsd da d++f++G
  lcl|FitnessBrowser__PS:Dsui_0011 234 TDAEAANLITSDYDANDKPFLTG 256
                                       **********************9 PP

  == domain 2  score: 277.3 bits;  conditional E-value: 1.1e-86
                         TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnWdkaledde 429
                                       ert+eGf+rvk+g+e++i+r+ a+aPyadlvW+et+ Pd+  a+efa++v++  P+kll+yn+sPsfnW+k+l+d +
  lcl|FitnessBrowser__PS:Dsui_0011 257 ERTQEGFFRVKNGLEQSISRGVAYAPYADLVWCETGVPDIGFAREFAQAVHAACPGKLLSYNCSPSFNWKKNLNDSQ 333
                                       8**************************************************************************** PP

                         TIGR01346 430 ikkfikelgdlGykfqfitlaGlhsealavfdlakdfak.eGmkayvekvqqrel...edGvdvlkhqkesGaeyfd 502
                                       i++f++el++lGyk+qfitlaG+h ++++ f++ak++a  eGmk+yve vq++e+   edG+++++hq+e+G++yfd
  lcl|FitnessBrowser__PS:Dsui_0011 334 IASFQEELSALGYKYQFITLAGIHVNWYNTFKFAKAYAGgEGMKHYVEMVQEPEFaarEDGYTFVSHQQEVGTGYFD 410
                                       **************************************99*****************99****************** PP

                         TIGR01346 503 qllklvqgGvsataalaksveedqf 527
                                       ++++++qgG s++ al++s+ee+qf
  lcl|FitnessBrowser__PS:Dsui_0011 411 DVTTVIQGGSSSVKALTGSTEEEQF 435
                                       ************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (436 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 0.00s 00:00:00.07 Elapsed: 00:00:00.07
# Mc/sec: 3.05
//
[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