Alignments for a candidate for aceA in Haloechinothrix alba DSM 45207

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Haloechinothrix alba DSM 45207

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_089299936.1 CHB84_RS03065 isocitrate lyase

Query= BRENDA::P9WKK7
         (428 letters)



>NCBI__GCF_900188115.1:WP_089299936.1
          Length = 428

 Score =  654 bits (1687), Expect = 0.0
 Identities = 311/420 (74%), Positives = 369/420 (87%), Gaps = 1/420 (0%)

Query: 8   KSAEQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDLEWVN 67
           ++A ++  +W+ NPRWK +TR YSA DVV L+GSVVEE+T ARRGAE LW+ L++ ++++
Sbjct: 10  QAAAELAADWENNPRWKGITRPYSAADVVKLRGSVVEENTYARRGAEKLWDLLNNEDYIH 69

Query: 68  ALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNA 127
           ALGALTGN AVQQVRAGL+AIYLSGWQVAGDANL+G TYPDQSLYPANSVP VVRRINNA
Sbjct: 70  ALGALTGNQAVQQVRAGLQAIYLSGWQVAGDANLAGQTYPDQSLYPANSVPAVVRRINNA 129

Query: 128 LQRADQIAKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLAS 187
           L RADQI   EGDTS++ W APIVAD EAGFGG LN +EL K +I+AG AG HWEDQLAS
Sbjct: 130 LARADQITWAEGDTSID-WFAPIVADAEAGFGGPLNAFELMKGMISAGAAGVHWEDQLAS 188

Query: 188 EKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDERDQP 247
           EKKCGHLGGKVL+PT+QH RTL +ARLAAD+A VP+++IARTDA+AATL+TSD+DERDQ 
Sbjct: 189 EKKCGHLGGKVLVPTKQHERTLNAARLAADIAGVPSLIIARTDAQAATLLTSDIDERDQK 248

Query: 248 FITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKAEYPD 307
            +TGERT EGFYR +NG++PCI R  AYAP++DL+WMET  PDL+ AR+F+EA+K +YPD
Sbjct: 249 HVTGERTSEGFYRVQNGLQPCIDRGLAYAPYSDLLWMETSEPDLDVARRFAEAIKDKYPD 308

Query: 308 QMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQ 367
           QMLAYNCSPSFNW+K+LDD+TIAKFQ+ELA MG+KFQFITLAGFHALNYSMFDLA GYA 
Sbjct: 309 QMLAYNCSPSFNWRKNLDDSTIAKFQRELAHMGYKFQFITLAGFHALNYSMFDLAKGYAT 368

Query: 368 NQMSAYVELQEREFAAEERGYTATKHQREVGAGYFDRIATTVDPNSSTTALTGSTEEGQF 427
             M+AYV+LQEREFAAEERGYTATKHQREVG G+FD+++T ++P SSTTALTGSTEE QF
Sbjct: 369 EDMTAYVDLQEREFAAEERGYTATKHQREVGTGWFDQVSTVLNPESSTTALTGSTEEAQF 428


Lambda     K      H
   0.316    0.130    0.384 

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: 700
Number of extensions: 18
Number of successful extensions: 2
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: 428
Length of database: 428
Length adjustment: 32
Effective length of query: 396
Effective length of database: 396
Effective search space:   156816
Effective search space used:   156816
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 WP_089299936.1 CHB84_RS03065 (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.4966.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.2e-192  624.4   3.5   3.8e-109  351.4   0.3    2.0  2  lcl|NCBI__GCF_900188115.1:WP_089299936.1  CHB84_RS03065 isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900188115.1:WP_089299936.1  CHB84_RS03065 isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.4   0.3  3.8e-109  3.8e-109       2     254 ..      13     252 ..      12     253 .. 0.98
   2 !  275.1   0.3   5.1e-86   5.1e-86     353     527 .]     253     428 .]     251     428 .] 0.99

  Alignments for each domain:
  == domain 1  score: 351.4 bits;  conditional E-value: 3.8e-109
                                 TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpv 70 
                                               +e+ ++W+ ++rw++i+r+ysa dvvklrGsv ee++ ++++a+klw++l++e     ++++lGal+++
  lcl|NCBI__GCF_900188115.1:WP_089299936.1  13 AELAADWENNPRWKGITRPYSAADVVKLRGSVVEENTYARRGAEKLWDLLNNE----DYIHALGALTGN 77 
                                               7999**********************************************865....47********** PP

                                 TIGR01346  71 qvsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakd 138
                                               q++qq++a l+a+ylsGWqv++danl+++++Pd+++yPa++vP++v+r+++al ++d++ + ++++   
  lcl|NCBI__GCF_900188115.1:WP_089299936.1  78 QAVQQVRAgLQAIYLSGWQVAGDANLAGQTYPDQSLYPANSVPAVVRRINNALARADQITWAEGDT--- 143
                                               *************************************************************99865... PP

                                 TIGR01346 139 eeelkelyidylvPivadadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqe 207
                                                       id++ Pivada+aGfGG l++f+l+k +i +Gaagvh+edql+sekkCGhl+Gkvlvp+++
  lcl|NCBI__GCF_900188115.1:WP_089299936.1 144 -------SIDWFAPIVADAEAGFGGPLNAFELMKGMISAGAAGVHWEDQLASEKKCGHLGGKVLVPTKQ 205
                                               .......49************************************************************ PP

                                 TIGR01346 208 hvnrlvaarlaadvmgvetllvartdaeaatlitsdvdardhefivG 254
                                               h ++l+aarlaad++gv+ l++artda+aatl+tsd+d+rd++ ++G
  lcl|NCBI__GCF_900188115.1:WP_089299936.1 206 HERTLNAARLAADIAGVPSLIIARTDAQAATLLTSDIDERDQKHVTG 252
                                               *********************************************99 PP

  == domain 2  score: 275.1 bits;  conditional E-value: 5.1e-86
                                 TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnW 421
                                               ert+eGfyrv++g++++i r+ a+aPy+dl+Wmets Pdl+ a++fae++k+k+Pd++layn+sPsfnW
  lcl|NCBI__GCF_900188115.1:WP_089299936.1 253 ERTSEGFYRVQNGLQPCIDRGLAYAPYSDLLWMETSEPDLDVARRFAEAIKDKYPDQMLAYNCSPSFNW 321
                                               8******************************************************************** PP

                                 TIGR01346 422 dkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvqqrel...edGv 487
                                                k+l+d +i+kf++el+++GykfqfitlaG+h+ ++++fdlak++a e m+ayv+ +q+re+   e+G+
  lcl|NCBI__GCF_900188115.1:WP_089299936.1 322 RKNLDDSTIAKFQRELAHMGYKFQFITLAGFHALNYSMFDLAKGYATEDMTAYVD-LQEREFaaeERGY 389
                                               *******************************************************.********99*** PP

                                 TIGR01346 488 dvlkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                               ++ khq+e+G+++fdq+ +++++  s+t+al++s+ee qf
  lcl|NCBI__GCF_900188115.1:WP_089299936.1 390 TATKHQREVGTGWFDQVSTVLNP-ESSTTALTGSTEEAQF 428
                                               ***********************.9**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (428 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 4.62
//
[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