Alignments for a candidate for xacD in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacD in Azospirillum brasilense Sp245

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate AZOBR_RS31260 AZOBR_RS31260 dihydroxy-acid dehydratase

Query= reanno::BFirm:BPHYT_RS19730
         (577 letters)



>FitnessBrowser__azobra:AZOBR_RS31260
          Length = 608

 Score =  471 bits (1212), Expect = e-137
 Identities = 271/592 (45%), Positives = 369/592 (62%), Gaps = 27/592 (4%)

Query: 11  LRSQAWFGLKDRDGF--LHRSWMKNQGIPHDEFD-GRPVIGICNTWSELTPCNAHFRELA 67
           LRS+AWF   D      L+     N G+  +E   G P+IGI  T S+L+PCN H   LA
Sbjct: 19  LRSRAWFDNPDNPDMTALYLERYLNFGLTREELQSGAPIIGIAQTGSDLSPCNRHHLVLA 78

Query: 68  EYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILLVGC 127
           E +++G+  AGG+ +EFPV  + ET  RPTA + RNLA + + E + G P+DGV+L +GC
Sbjct: 79  ERLREGIRTAGGIAIEFPVHPIQETGKRPTASIDRNLAYLGLVEVLHGYPLDGVVLTIGC 138

Query: 128 DKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQEEFT 187
           DKTTPA LM AA+ N+PA+A+S GPMLNG FRG+  GSGT VW+  + + AG +  + F 
Sbjct: 139 DKTTPACLMAAATVNIPAIALSVGPMLNGWFRGERTGSGTIVWKARQMMAAGEIDYQGFI 198

Query: 188 EAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIVDM 247
           E  +    S G+C TMGTASTM S+ E LGM LP +AAIPA    RQ   +  G+RIV+M
Sbjct: 199 ELVASSAPSTGYCNTMGTASTMNSLAEVLGMQLPGSAAIPAPYRERQQADYETGKRIVEM 258

Query: 248 VREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWEL-GSNVP 306
           VREDL    ILTR AF NAI  N+AIGGSTNA +H+ A+AK IGV L++EDW+  G +VP
Sbjct: 259 VREDLKPSDILTRDAFLNAIVVNSAIGGSTNAPIHINAIAKHIGVPLTVEDWQTHGHDVP 318

Query: 307 CLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAANYDEK 366
            LVNLQP+GEYL EDF+ AGG+PAV+ QL  +GL+ + A TVNG+T+ +N R     D +
Sbjct: 319 LLVNLQPAGEYLGEDFHRAGGVPAVVAQLMGKGLIREGAPTVNGRTIGENCRRQPILDTR 378

Query: 367 VITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKHR------------GRAVVF 414
           VI    EP  P AG  VL+GNL   GA I  ++  +   + R            G+ VVF
Sbjct: 379 VIHPIDEPLMPNAGFVVLRGNLF--GAAIMKTSVISDEFRERYLSNPQDPEAFEGKVVVF 436

Query: 415 ENIEELHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRIS 474
           +  E+ H +IDD SL ID + I+V++G GP GYPG AEV NM  P  ++++G+  +  I 
Sbjct: 437 DGPEDYHHRIDDPSLGIDAYTILVIRGTGPIGYPGAAEVVNMRPPATLIKQGVHSLPCIG 496

Query: 475 DGRMSGTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAW 534
           DGR SGT+    +L+ SPEAAAGG LA +++GD + +D+      + + + ELA RRAA 
Sbjct: 497 DGRQSGTSGSPSILNASPEAAAGGGLALLRSGDRVRIDLRRGSADILIPEGELADRRAAL 556

Query: 535 QA----PEAPKRGYYKLYVEHVL-QADQGADLDFLVG----SSGAPVPRDSH 577
           +A    P  P +  ++     ++ Q D+G  L   V     +    +PRD+H
Sbjct: 557 EAAGGYPIPPSQTPWQEIQRGIVDQLDEGMVLKPAVKYQRVAQTMGIPRDNH 608


Lambda     K      H
   0.318    0.135    0.401 

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: 975
Number of extensions: 59
Number of successful extensions: 4
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: 577
Length of database: 608
Length adjustment: 37
Effective length of query: 540
Effective length of database: 571
Effective search space:   308340
Effective search space used:   308340
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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

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 catabolism of small carbon sources