Alignments for a candidate for leuA in Desulfovibrio oxyclinae DSM 11498

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Desulfovibrio oxyclinae DSM 11498

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_018123428.1 B149_RS0101700 2-isopropylmalate synthase

Query= BRENDA::Q9JZG1
         (517 letters)



>NCBI__GCF_000375485.1:WP_018123428.1
          Length = 512

 Score =  480 bits (1235), Expect = e-140
 Identities = 256/513 (49%), Positives = 351/513 (68%), Gaps = 8/513 (1%)

Query: 4   TNRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAI 63
           +++++IFDTTLRDGEQSPGA M  +EKIR+ARQLE LGVDIIEAGF  AS GDFE+V +I
Sbjct: 2   SDKIMIFDTTLRDGEQSPGATMNIDEKIRMARQLETLGVDIIEAGFPIASQGDFESVKSI 61

Query: 64  AKTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEA 123
           A+++T   V  L R++ +DI +  EAV  AP+ RIHTF+ATSPIHMEYKL   P QV+E 
Sbjct: 62  AESVTNLQVAGLCRSVTKDIDRCWEAVKNAPEGRIHTFLATSPIHMEYKLGKTPDQVVEM 121

Query: 124 AVKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTE 183
           A  AVK A +YT +VEFS EDA RS+ DFL  +    I+AGA T+N+PDTVGY+ P++  
Sbjct: 122 AEAAVKHAAKYTSNVEFSAEDASRSDWDFLVRVFNTAIKAGARTLNVPDTVGYTQPHEFY 181

Query: 184 EFFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNASV 243
           E  R L+ K       V S HCHNDLGLAVANSLAA++ GARQVECTV+G+GERAGNA++
Sbjct: 182 EMIRFLMEKLEMKSDTVISVHCHNDLGLAVANSLAAIRAGARQVECTVSGIGERAGNAAL 241

Query: 244 EEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIHQ 303
           EE+VMAL  R DL+ ++  + T Q+ PS + +S I G P+ P KAIVG NAF+HESG+HQ
Sbjct: 242 EEVVMALNTRKDLYDIDCDVVTEQLYPSCRRLSQIIGQPIPPYKAIVGTNAFAHESGVHQ 301

Query: 304 DGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFARF 363
           DGV+K+R+TYEIM+AES+G     + +GK SG +A K K+ +LG  L+ ++ + A F+  
Sbjct: 302 DGVIKNRQTYEIMTAESIGRQGTEIVIGKHSGSHAIKRKVEELGYTLQDDQ-VEAMFSAV 360

Query: 364 KELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIKGEE-- 421
           KELADKK  I DED+ ALV +++     + ++     + + TGE P    V    G+E  
Sbjct: 361 KELADKKERIHDEDVEALVLEKV-YRRRDKFRLRDMSVFSGTGEVPPHAAVVMEFGDEGG 419

Query: 422 ----KRASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRV 477
               ++ +A G G +DA+F +I  +    A+L+ Y+VNAVT GT++    +VR+      
Sbjct: 420 DVEVRKNTAFGRGTIDAVFSSIYDLIGYRASLESYTVNAVTSGTDALAGVAVRITHDGFK 479

Query: 478 VNGQGADTDVLVATAKAYLSALSKLEFSAAKPK 510
             G+  D DV+ A+A A ++AL++LE +  + K
Sbjct: 480 AVGRANDEDVVRASALALVNALNRLEITREERK 512


Lambda     K      H
   0.313    0.129    0.352 

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: 633
Number of extensions: 25
Number of successful extensions: 3
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: 517
Length of database: 512
Length adjustment: 35
Effective length of query: 482
Effective length of database: 477
Effective search space:   229914
Effective search space used:   229914
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate WP_018123428.1 B149_RS0101700 (2-isopropylmalate synthase)
to HMM TIGR00973 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))

# 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/TIGR00973.hmm
# target sequence database:        /tmp/gapView.26961.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00973  [M=494]
Accession:   TIGR00973
Description: leuA_bact: 2-isopropylmalate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.2e-203  660.1   4.0     1e-202  659.9   4.0    1.0  1  lcl|NCBI__GCF_000375485.1:WP_018123428.1  B149_RS0101700 2-isopropylmalate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000375485.1:WP_018123428.1  B149_RS0101700 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  659.9   4.0    1e-202    1e-202       1     494 []       4     502 ..       4     502 .. 0.97

  Alignments for each domain:
  == domain 1  score: 659.9 bits;  conditional E-value: 1e-202
                                 TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvg 69 
                                               +++ifdttlrdGeq+pga+++++ek+++a++le lgvdiieaGfp++s+gdfe+v+ ia++v n +v+g
  lcl|NCBI__GCF_000375485.1:WP_018123428.1   4 KIMIFDTTLRDGEQSPGATMNIDEKIRMARQLETLGVDIIEAGFPIASQGDFESVKSIAESVTNLQVAG 72 
                                               79******************************************************************* PP

                                 TIGR00973  70 laravekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsae 138
                                               l+r+v kdid  +ea+k+a + rihtf+ats+ih+e+kl kt d+v+e++++avk+a +++ +vefsae
  lcl|NCBI__GCF_000375485.1:WP_018123428.1  73 LCRSVTKDIDRCWEAVKNAPEGRIHTFLATSPIHMEYKLGKTPDQVVEMAEAAVKHAAKYTSNVEFSAE 141
                                               ********************************************************************* PP

                                 TIGR00973 139 dagrteleflarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGla 207
                                               da+r++ +fl+rv+++ai+aGa t+n+PdtvGy+ P+e+ e+i+ l+e++    ++++svhch+dlGla
  lcl|NCBI__GCF_000375485.1:WP_018123428.1 142 DASRSDWDFLVRVFNTAIKAGARTLNVPDTVGYTQPHEFYEMIRFLMEKLEMKSDTVISVHCHNDLGLA 210
                                               ********************************************************************* PP

                                 TIGR00973 208 vanslaavknGarqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgm 276
                                               vanslaa+++Garqvect+ GiGeraGnaaleevvmal++rkd+++++ ++ t+++y + r +s++ g 
  lcl|NCBI__GCF_000375485.1:WP_018123428.1 211 VANSLAAIRAGARQVECTVSGIGERAGNAALEEVVMALNTRKDLYDIDCDVVTEQLYPSCRRLSQIIGQ 279
                                               ********************************************************************* PP

                                 TIGR00973 277 lvqrnkaivGdnafahesGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkl 345
                                               ++++ kaivG nafahesG+hqdGv+kn++tyei+++esiG++ +++v+gk+sG +a+k+++eelG+ l
  lcl|NCBI__GCF_000375485.1:WP_018123428.1 280 PIPPYKAIVGTNAFAHESGVHQDGVIKNRQTYEIMTAESIGRQGTEIVIGKHSGSHAIKRKVEELGYTL 348
                                               ********************************************************************* PP

                                 TIGR00973 346 deeeldklfekfkeladkkkevfdedlealvleelrqeeeeklkleklqvqsgeesv.ptatvklkvkg 413
                                               ++++++ +f++ keladkk++++ded+ealvle++ + +++k++l  ++v sg+ +v p a+v +++ +
  lcl|NCBI__GCF_000375485.1:WP_018123428.1 349 QDDQVEAMFSAVKELADKKERIHDEDVEALVLEKVYR-RRDKFRLRDMSVFSGTGEVpPHAAVVMEFGD 416
                                               *********************************9995.6667**********9977626899***9974 PP

                                 TIGR00973 414 e....e.keaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvlelngkkysGrgv 477
                                               e    e ++++a G G++dav+ +i  ++++   l+ y+++a+++g+dal+ v v+++++g k+ Gr+ 
  lcl|NCBI__GCF_000375485.1:WP_018123428.1 417 EggdvEvRKNTAFGRGTIDAVFSSIYDLIGYRASLESYTVNAVTSGTDALAGVAVRITHDGFKAVGRAN 485
                                               322223688999********************************************************* PP

                                 TIGR00973 478 atdiveasakayvnaln 494
                                               + d+v+asa a+vnaln
  lcl|NCBI__GCF_000375485.1:WP_018123428.1 486 DEDVVRASALALVNALN 502
                                               ****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (512 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.17
//
[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