Alignments for a candidate for aceA in Thioalkalivibrio paradoxus ARh 1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Thioalkalivibrio paradoxus ARh 1

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_006748562.1 THITH_RS05895 isocitrate lyase

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



>NCBI__GCF_000227685.2:WP_006748562.1
          Length = 440

 Score =  727 bits (1877), Expect = 0.0
 Identities = 350/433 (80%), Positives = 388/433 (89%)

Query: 10  SREQQIAALEKDWATNPRWKGVKRGYSAADVVRLRGSLPIEHTLAKRGAEKLWDKINGGA 69
           SREQQI ALE++WA  PRW+GV+RGYSAADVVRLRGS+  E++ A+ GAEKLW +++GGA
Sbjct: 8   SREQQIHALEQEWAEQPRWQGVRRGYSAADVVRLRGSVRPEYSYARMGAEKLWQRLHGGA 67

Query: 70  KKGYVNAFGAISAGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLYAYDSVPTMV 129
           +KGYVNA G ++ GQA+QQA+AGLEA+YLSGWQVAADGNTSETMYPDQSLYAYDSVP MV
Sbjct: 68  RKGYVNALGTLTGGQALQQARAGLEAIYLSGWQVAADGNTSETMYPDQSLYAYDSVPAMV 127

Query: 130 RRINNTFKRADEIQWGRGINPGDKEFIDYFLPIVADAEAGFGGVLNAFELMKNMIQSGAA 189
           RRINN F+R DEIQW RGI PGD  ++DYFLPIVADAEAGFGGVLNAFELMKNMI +GAA
Sbjct: 128 RRINNAFQRGDEIQWSRGIGPGDDGYVDYFLPIVADAEAGFGGVLNAFELMKNMIVAGAA 187

Query: 190 GVHFEDQLAAVKKCGHMGGKVLVPTQEACEKLISARFAADVMGVSTIVLARTDAEAANLI 249
           GVHFEDQLAAVKKCGHMGGKVLVPTQEA +KLI+AR AADVMGV TI+LARTDAEAANL+
Sbjct: 188 GVHFEDQLAAVKKCGHMGGKVLVPTQEAVQKLIAARLAADVMGVPTILLARTDAEAANLL 247

Query: 250 TSDHDANDKPFLTGERTQEGFYRVKNGLEQAISRGVAYAPYADLVWCETGVPDIGFAREF 309
           TSD D ND+PFLTG+RT EGF+RV+NGLEQAISRGVAYAPYADLVWCETG PD+GFAREF
Sbjct: 248 TSDVDDNDRPFLTGQRTSEGFFRVRNGLEQAISRGVAYAPYADLVWCETGTPDLGFAREF 307

Query: 310 AQAVHAACPGKLLSYNCSPSFNWKKNLNDKQIASFQEDLSALGYKYQFITLAGIHINWFN 369
           AQAV A  P +LL+YNCSPSFNWKKNL D QIASFQ++LS LGYKYQFITLAGIH  WFN
Sbjct: 308 AQAVRAENPNQLLAYNCSPSFNWKKNLTDAQIASFQDELSTLGYKYQFITLAGIHSMWFN 367

Query: 370 TFQFAHAYANGEGMKHYVNMVQEPEFAARDKGYTFVSHQQEVGAGYFDDVTTVIQGGSSS 429
            F  AH YA GEGM+HYV  VQ+PEFAAR++GYTFVSHQQEVGAGYFDDVTTVIQGG SS
Sbjct: 368 MFDLAHDYARGEGMRHYVEKVQQPEFAARERGYTFVSHQQEVGAGYFDDVTTVIQGGGSS 427

Query: 430 VKALTGSTEEEQF 442
           V AL GSTEEEQF
Sbjct: 428 VTALKGSTEEEQF 440


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: 780
Number of extensions: 30
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: 443
Length of database: 440
Length adjustment: 32
Effective length of query: 411
Effective length of database: 408
Effective search space:   167688
Effective search space used:   167688
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_006748562.1 THITH_RS05895 (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.805.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.9e-202  657.6   1.3   1.1e-112  363.0   0.0    2.0  2  lcl|NCBI__GCF_000227685.2:WP_006748562.1  THITH_RS05895 isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000227685.2:WP_006748562.1  THITH_RS05895 isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  363.0   0.0  1.1e-112  1.1e-112       3     254 ..      15     261 ..      13     263 .. 0.98
   2 !  294.3   0.4   7.5e-92   7.5e-92     353     527 .]     262     440 .]     262     440 .] 0.99

  Alignments for each domain:
  == domain 1  score: 363.0 bits;  conditional E-value: 1.1e-112
                                 TIGR01346   3 eiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpvq 71 
                                                +++eW  ++rw++++r ysa dvv+lrGsvr+e   ++++a+klw+ l+     k+++++lG+l+++q
  lcl|NCBI__GCF_000227685.2:WP_006748562.1  15 ALEQEWAEQPRWQGVRRGYSAADVVRLRGSVRPEYSYARMGAEKLWQRLHGGAR-KGYVNALGTLTGGQ 82 
                                               689***********************************************9887.6************* PP

                                 TIGR01346  72 vsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakde 139
                                               ++qqa+a l+a+ylsGWqv++d n+s+ ++Pd+++y +d+vP+ v+r+++a+++ d++q++ ++ + d+
  lcl|NCBI__GCF_000227685.2:WP_006748562.1  83 ALQQARAgLEAIYLSGWQVAADGNTSETMYPDQSLYAYDSVPAMVRRINNAFQRGDEIQWSRGIGPGDD 151
                                               ******************************************************************999 PP

                                 TIGR01346 140 eelkelyidylvPivadadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqeh 208
                                                     y+dy++Pivada+aGfGGvl++f+l+k +i +Gaagvh+edql+++kkCGh++Gkvlvp+qe+
  lcl|NCBI__GCF_000227685.2:WP_006748562.1 152 -----GYVDYFLPIVADAEAGFGGVLNAFELMKNMIVAGAAGVHFEDQLAAVKKCGHMGGKVLVPTQEA 215
                                               .....7*************************************************************** PP

                                 TIGR01346 209 vnrlvaarlaadvmgvetllvartdaeaatlitsdvdardhefivG 254
                                               v++l+aarlaadvmgv+t+l+artdaeaa+l+tsdvd+ d++f++G
  lcl|NCBI__GCF_000227685.2:WP_006748562.1 216 VQKLIAARLAADVMGVPTILLARTDAEAANLLTSDVDDNDRPFLTG 261
                                               *********************************************9 PP

  == domain 2  score: 294.3 bits;  conditional E-value: 7.5e-92
                                 TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnW 421
                                               +rt+eGf+rv++g+e+ai+r+ a+aPyadlvW+et+tPdl  a+efa++v+++ P++llayn+sPsfnW
  lcl|NCBI__GCF_000227685.2:WP_006748562.1 262 QRTSEGFFRVRNGLEQAISRGVAYAPYADLVWCETGTPDLGFAREFAQAVRAENPNQLLAYNCSPSFNW 330
                                               59******************************************************************* PP

                                 TIGR01346 422 dkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfak.eGmkayvekvqqrel...edG 486
                                               +k+l+d +i++f++el+ lGyk+qfitlaG+hs+++++fdla+d+a+ eGm++yvekvqq+e+   e+G
  lcl|NCBI__GCF_000227685.2:WP_006748562.1 331 KKNLTDAQIASFQDELSTLGYKYQFITLAGIHSMWFNMFDLAHDYARgEGMRHYVEKVQQPEFaarERG 399
                                               ****************************************************************999** PP

                                 TIGR01346 487 vdvlkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                               +++++hq+e+Ga+yfd++++++qgG s+++al++s+ee+qf
  lcl|NCBI__GCF_000227685.2:WP_006748562.1 400 YTFVSHQQEVGAGYFDDVTTVIQGGGSSVTALKGSTEEEQF 440
                                               ****************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (440 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 0.01s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 4.26
//
[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