Alignments for a candidate for aceA in Thioalkalivibrio denitrificans ALJD

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Thioalkalivibrio denitrificans ALJD

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_077279119.1 B1C78_RS10515 isocitrate lyase

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



>NCBI__GCF_002000365.1:WP_077279119.1
          Length = 439

 Score =  732 bits (1889), Expect = 0.0
 Identities = 354/434 (81%), Positives = 390/434 (89%)

Query: 9   LSREQQIAALEKDWATNPRWKGVKRGYSAADVVRLRGSLPIEHTLAKRGAEKLWDKINGG 68
           +SREQQI ALE+DWA NPRW+GVKRGY+AADVVRLRGS+  EHT+A+RGAEKLW  +NG 
Sbjct: 1   MSREQQIQALERDWAENPRWQGVKRGYTAADVVRLRGSVQPEHTIARRGAEKLWRLVNGD 60

Query: 69  AKKGYVNAFGAISAGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLYAYDSVPTM 128
           AKKGYVN  GA++AGQA+QQAKAG+EA+YLSGWQVAAD NTSETMYPDQSLYAYDSVPT+
Sbjct: 61  AKKGYVNCLGALTAGQALQQAKAGVEAIYLSGWQVAADNNTSETMYPDQSLYAYDSVPTV 120

Query: 129 VRRINNTFKRADEIQWGRGINPGDKEFIDYFLPIVADAEAGFGGVLNAFELMKNMIQSGA 188
           VRRINNTFKRADEIQW RG++P D+  ID+FLPIVADAEAGFGGVLNAFELMKNMI +GA
Sbjct: 121 VRRINNTFKRADEIQWSRGVSPEDENGIDFFLPIVADAEAGFGGVLNAFELMKNMITAGA 180

Query: 189 AGVHFEDQLAAVKKCGHMGGKVLVPTQEACEKLISARFAADVMGVSTIVLARTDAEAANL 248
           +GVHFEDQLAAVKKCGHMGGKVLVPTQEA +KL++AR AADVMGV T++LARTDAEAANL
Sbjct: 181 SGVHFEDQLAAVKKCGHMGGKVLVPTQEAVQKLVAARLAADVMGVPTLLLARTDAEAANL 240

Query: 249 ITSDHDANDKPFLTGERTQEGFYRVKNGLEQAISRGVAYAPYADLVWCETGVPDIGFARE 308
           +TSD D ND+PFLTGERT EGFYRVKNGLEQAISRGVAYAPYADLVWCETG PD+GFARE
Sbjct: 241 LTSDVDDNDRPFLTGERTAEGFYRVKNGLEQAISRGVAYAPYADLVWCETGTPDLGFARE 300

Query: 309 FAQAVHAACPGKLLSYNCSPSFNWKKNLNDKQIASFQEDLSALGYKYQFITLAGIHINWF 368
           FA+AV    PG+LL+YNCSPSFNWKKNL+ K IA FQ+ LS  GYKYQFITLAGIH  WF
Sbjct: 301 FAEAVRDKNPGQLLAYNCSPSFNWKKNLDMKTIAEFQDKLSEYGYKYQFITLAGIHSMWF 360

Query: 369 NTFQFAHAYANGEGMKHYVNMVQEPEFAARDKGYTFVSHQQEVGAGYFDDVTTVIQGGSS 428
           N F  AH YA GEGM+HYV  VQEPEFAAR+KGYTFVSHQQEVGAGYFDDVTT IQGG+S
Sbjct: 361 NMFDLAHDYARGEGMRHYVEKVQEPEFAAREKGYTFVSHQQEVGAGYFDDVTTTIQGGAS 420

Query: 429 SVKALTGSTEEEQF 442
           SV ALTGSTEE QF
Sbjct: 421 SVTALTGSTEEAQF 434


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: 758
Number of extensions: 26
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: 439
Length adjustment: 32
Effective length of query: 411
Effective length of database: 407
Effective search space:   167277
Effective search space used:   167277
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_077279119.1 B1C78_RS10515 (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.30580.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-203  660.8   3.1     9e-115  369.9   0.1    2.0  2  lcl|NCBI__GCF_002000365.1:WP_077279119.1  B1C78_RS10515 isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002000365.1:WP_077279119.1  B1C78_RS10515 isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.9   0.1    9e-115    9e-115       2     254 ..       8     255 ..       7     257 .. 0.98
   2 !  292.4   0.6   2.8e-91   2.8e-91     353     527 .]     256     434 ..     255     434 .. 0.99

  Alignments for each domain:
  == domain 1  score: 369.9 bits;  conditional E-value: 9e-115
                                 TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpv 70 
                                               + ++++W  ++rw+++kr y+a dvv+lrGsv++e+++++++a+klwr+++ + k k+++++lGal+++
  lcl|NCBI__GCF_002000365.1:WP_077279119.1   8 QALERDWAENPRWQGVKRGYTAADVVRLRGSVQPEHTIARRGAEKLWRLVNGDAK-KGYVNCLGALTAG 75 
                                               6789***********************************************9998.6************ PP

                                 TIGR01346  71 qvsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakd 138
                                               q++qqaka ++a+ylsGWqv++d+n+s+ ++Pd+++y +d+vP++v+r++++++++d++q++ + +++d
  lcl|NCBI__GCF_002000365.1:WP_077279119.1  76 QALQQAKAgVEAIYLSGWQVAADNNTSETMYPDQSLYAYDSVPTVVRRINNTFKRADEIQWSRGVSPED 144
                                               ******************************************************************999 PP

                                 TIGR01346 139 eeelkelyidylvPivadadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqe 207
                                               e       id+++Pivada+aGfGGvl++f+l+k +i +Ga+gvh+edql+++kkCGh++Gkvlvp+qe
  lcl|NCBI__GCF_002000365.1:WP_077279119.1 145 E-----NGIDFFLPIVADAEAGFGGVLNAFELMKNMITAGASGVHFEDQLAAVKKCGHMGGKVLVPTQE 208
                                               8.....589************************************************************ PP

                                 TIGR01346 208 hvnrlvaarlaadvmgvetllvartdaeaatlitsdvdardhefivG 254
                                               +v++lvaarlaadvmgv+tll+artdaeaa+l+tsdvd+ d++f++G
  lcl|NCBI__GCF_002000365.1:WP_077279119.1 209 AVQKLVAARLAADVMGVPTLLLARTDAEAANLLTSDVDDNDRPFLTG 255
                                               **********************************************9 PP

  == domain 2  score: 292.4 bits;  conditional E-value: 2.8e-91
                                 TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnW 421
                                               ert+eGfyrvk+g+e+ai+r+ a+aPyadlvW+et+tPdl  a+efae+v++k P++llayn+sPsfnW
  lcl|NCBI__GCF_002000365.1:WP_077279119.1 256 ERTAEGFYRVKNGLEQAISRGVAYAPYADLVWCETGTPDLGFAREFAEAVRDKNPGQLLAYNCSPSFNW 324
                                               8******************************************************************** PP

                                 TIGR01346 422 dkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfak.eGmkayvekvqqrel...edG 486
                                               +k+l+ ++i++f+++l++ Gyk+qfitlaG+hs+++++fdla+d+a+ eGm++yvekvq++e+   e+G
  lcl|NCBI__GCF_002000365.1:WP_077279119.1 325 KKNLDMKTIAEFQDKLSEYGYKYQFITLAGIHSMWFNMFDLAHDYARgEGMRHYVEKVQEPEFaarEKG 393
                                               ****************************************************************999** PP

                                 TIGR01346 487 vdvlkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                               +++++hq+e+Ga+yfd++++++qgG s+++al++s+ee qf
  lcl|NCBI__GCF_002000365.1:WP_077279119.1 394 YTFVSHQQEVGAGYFDDVTTTIQGGASSVTALTGSTEEAQF 434
                                               ****************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (439 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: 00:00:00.05
# Mc/sec: 4.59
//
[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