Alignments for a candidate for aceA in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Hydrogenophaga taeniospiralis NBRC 102512

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_068175541.1 HTA01S_RS22560 isocitrate lyase

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



>NCBI__GCF_001592305.1:WP_068175541.1
          Length = 443

 Score =  861 bits (2225), Expect = 0.0
 Identities = 420/443 (94%), Positives = 431/443 (97%)

Query: 1   MPQSLNEQLSREQQIAALEKDWATNPRWKGVKRGYSAADVVRLRGSLPIEHTLAKRGAEK 60
           MPQ+LNEQLSR+QQI ALEKDWATNPRWKGVKRGYSAADVVRLRGS+ +EHTLA RGAEK
Sbjct: 1   MPQALNEQLSRQQQIDALEKDWATNPRWKGVKRGYSAADVVRLRGSMQVEHTLAMRGAEK 60

Query: 61  LWDKINGGAKKGYVNAFGAISAGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLY 120
           LWDK+NGGAKKGYVNAFGAISAGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLY
Sbjct: 61  LWDKVNGGAKKGYVNAFGAISAGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLY 120

Query: 121 AYDSVPTMVRRINNTFKRADEIQWGRGINPGDKEFIDYFLPIVADAEAGFGGVLNAFELM 180
           AYDSVPTMVRRINNTFKRADEIQWGRGI PG  EFIDYFLPIVADAEAGFGGVLNAFELM
Sbjct: 121 AYDSVPTMVRRINNTFKRADEIQWGRGIEPGSPEFIDYFLPIVADAEAGFGGVLNAFELM 180

Query: 181 KNMIQSGAAGVHFEDQLAAVKKCGHMGGKVLVPTQEACEKLISARFAADVMGVSTIVLAR 240
           KNMI +GAAGVHFEDQLAAVKKCGHMGGKVLVPTQEACEKLI+ARFAADVMGVSTIVLAR
Sbjct: 181 KNMITAGAAGVHFEDQLAAVKKCGHMGGKVLVPTQEACEKLIAARFAADVMGVSTIVLAR 240

Query: 241 TDAEAANLITSDHDANDKPFLTGERTQEGFYRVKNGLEQAISRGVAYAPYADLVWCETGV 300
           TDAEAANLITSDHDANDKPFLTGERTQEGFYRVKNGLEQAISRG+AYAPYADLVWCETGV
Sbjct: 241 TDAEAANLITSDHDANDKPFLTGERTQEGFYRVKNGLEQAISRGIAYAPYADLVWCETGV 300

Query: 301 PDIGFAREFAQAVHAACPGKLLSYNCSPSFNWKKNLNDKQIASFQEDLSALGYKYQFITL 360
           PDIGFAREFAQAV  ACPGKLLSYNCSPSFNWKKNL+DKQIASFQEDL+ALGYKYQFITL
Sbjct: 301 PDIGFAREFAQAVQGACPGKLLSYNCSPSFNWKKNLDDKQIASFQEDLAALGYKYQFITL 360

Query: 361 AGIHINWFNTFQFAHAYANGEGMKHYVNMVQEPEFAARDKGYTFVSHQQEVGAGYFDDVT 420
           AGIHINWFNTFQFAHAYA GEGMKHY  MVQEPEFAAR+KGYTFVSHQQEVGAGYFDDVT
Sbjct: 361 AGIHINWFNTFQFAHAYARGEGMKHYTEMVQEPEFAAREKGYTFVSHQQEVGAGYFDDVT 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: 823
Number of extensions: 25
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 WP_068175541.1 HTA01S_RS22560 (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.10070.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.6e-194  631.6   4.7   1.5e-111  359.3   0.2    2.0  2  lcl|NCBI__GCF_001592305.1:WP_068175541.1  HTA01S_RS22560 isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001592305.1:WP_068175541.1  HTA01S_RS22560 isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.3   0.2  1.5e-111  1.5e-111       2     254 ..      16     263 ..      15     265 .. 0.98
   2 !  274.9   0.8   5.6e-86   5.6e-86     353     527 .]     264     442 ..     264     442 .. 1.00

  Alignments for each domain:
  == domain 1  score: 359.3 bits;  conditional E-value: 1.5e-111
                                 TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpv 70 
                                               + ++k+W t++rw+++kr ysa dvv+lrGs++ e++l+ ++a+klw+ ++   k k++++++Ga+ ++
  lcl|NCBI__GCF_001592305.1:WP_068175541.1  16 DALEKDWATNPRWKGVKRGYSAADVVRLRGSMQVEHTLAMRGAEKLWDKVNGGAK-KGYVNAFGAISAG 83 
                                               5689**********************************************99887.6************ PP

                                 TIGR01346  71 qvsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakd 138
                                               q++qqaka l+avylsGWqv++d n+s+ ++Pd+++y +d+vP+ v+r++++++++d++q+  ++++ +
  lcl|NCBI__GCF_001592305.1:WP_068175541.1  84 QAMQQAKAgLEAVYLSGWQVAADGNTSETMYPDQSLYAYDSVPTMVRRINNTFKRADEIQWGRGIEPGS 152
                                               ********************************************************************* PP

                                 TIGR01346 139 eeelkelyidylvPivadadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqe 207
                                               +      +idy++Pivada+aGfGGvl++f+l+k +i +Gaagvh+edql+++kkCGh++Gkvlvp+qe
  lcl|NCBI__GCF_001592305.1:WP_068175541.1 153 P-----EFIDYFLPIVADAEAGFGGVLNAFELMKNMITAGAAGVHFEDQLAAVKKCGHMGGKVLVPTQE 216
                                               9.....49************************************************************* PP

                                 TIGR01346 208 hvnrlvaarlaadvmgvetllvartdaeaatlitsdvdardhefivG 254
                                               + ++l+aar+aadvmgv t+++artdaeaa+litsd da d++f++G
  lcl|NCBI__GCF_001592305.1:WP_068175541.1 217 ACEKLIAARFAADVMGVSTIVLARTDAEAANLITSDHDANDKPFLTG 263
                                               **********************************************9 PP

  == domain 2  score: 274.9 bits;  conditional E-value: 5.6e-86
                                 TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnW 421
                                               ert+eGfyrvk+g+e+ai+r+ a+aPyadlvW+et+ Pd+  a+efa++v+   P+kll+yn+sPsfnW
  lcl|NCBI__GCF_001592305.1:WP_068175541.1 264 ERTQEGFYRVKNGLEQAISRGIAYAPYADLVWCETGVPDIGFAREFAQAVQGACPGKLLSYNCSPSFNW 332
                                               7******************************************************************** PP

                                 TIGR01346 422 dkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfak.eGmkayvekvqqrel...edG 486
                                               +k+l+d++i++f+++l++lGyk+qfitlaG+h ++++ f++a+++a+ eGmk+y e vq++e+   e+G
  lcl|NCBI__GCF_001592305.1:WP_068175541.1 333 KKNLDDKQIASFQEDLAALGYKYQFITLAGIHINWFNTFQFAHAYARgEGMKHYTEMVQEPEFaarEKG 401
                                               ****************************************************************999** PP

                                 TIGR01346 487 vdvlkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                               +++++hq+e+Ga+yfd++++++qgG s++ al++s+ee+qf
  lcl|NCBI__GCF_001592305.1:WP_068175541.1 402 YTFVSHQQEVGAGYFDDVTTVIQGGSSSVKALTGSTEEEQF 442
                                               ****************************************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: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 4.41
//
[ok]

This GapMind analysis is from Apr 10 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