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_RS15015 AZOBR_RS15015 dihydroxy-acid dehydratase

Query= reanno::Smeli:SM_b20890
         (579 letters)



>FitnessBrowser__azobra:AZOBR_RS15015
          Length = 621

 Score =  275 bits (703), Expect = 4e-78
 Identities = 203/570 (35%), Positives = 297/570 (52%), Gaps = 66/570 (11%)

Query: 21  GKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGF 80
           G+N    R   +  G+    F G+PII I N++++  P + HL+DL + V R + +AGG 
Sbjct: 12  GRNMAGARGLWRATGMKDGDF-GKPIIAIANSFTQFVPGHVHLKDLGQLVAREIEKAGGV 70

Query: 81  PVEFPVFSTGES-TLRPTAMMF----RNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLL 135
             EF   +  +   +    M++    R L A  VE  +  +  D +V +  CDK TP +L
Sbjct: 71  AKEFNTIAVDDGIAMGHDGMLYSLPSRELIADAVEYMVNAHCADALVCISNCDKITPGML 130

Query: 136 MGAASVDIPAIVVSGGPMLNGK--WRGKDVGSGTAIWQFSEMVKSGE--MSLEEFMDAEQ 191
           M A  ++IPA+ VSGGPM  GK  WRGK      A+     MV + +  +S EE    E+
Sbjct: 131 MAAMRLNIPAVFVSGGPMEAGKVNWRGKT----KAVDLIDAMVAAADPTVSDEEAAVMER 186

Query: 192 GMARSAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVK-- 249
           G   + GSC  M TA++M  + EALG++L GN  I A  A R+ +    GR  VE+ +  
Sbjct: 187 GSCPTCGSCSGMFTANSMNCLTEALGLSLPGNGTILATHADRKELFLAAGRMAVELCRRW 246

Query: 250 ---EDLK--PSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGR 304
              ED    P  I T EAFENA+ ++ A+GGSTN VLHLLA A    V  ++ D DRL R
Sbjct: 247 YQEEDATALPRGIATFEAFENAMTLDIAMGGSTNTVLHLLAAAQEGQVPFTMADIDRLSR 306

Query: 305 DVPTIVNLQPS-GKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWN-----DV 358
            VP +  + P+     +E+ + AGG+  ++  +   GLL+ D  TV   T+ +     DV
Sbjct: 307 RVPNVCKVAPAVSDVHIEDVHKAGGIFGILGELDRGGLLNRDVATVHAKTLGDALDRWDV 366

Query: 359 K-----GV---------------------------VNYNEDVILPREKALTKSGGIAVLR 386
           K     GV                           ++ ++ VI   + A +K GG+AVL 
Sbjct: 367 KRTQDEGVHTMFKAAPGGIPTTIAFSQEKRWPELDLDRDKGVIRSVDSAFSKDGGLAVLF 426

Query: 387 GNLAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDIDETCIMVLKYCGPK 446
           GN+A +G ++K +      +   G A VFES +     I  + +   +  ++V++Y GP+
Sbjct: 427 GNIAEKGCIVKTAGVDASNLVFAGPARVFESQDAAVEAILGDTVKAGD--VVVIRYEGPR 484

Query: 447 GYPGMAEVGNMGLPPKVLK-KGITDMIR-ISDARMSGTAYGTVILHTAPEAAEGGPLALV 504
           G PGM E   M  P   LK KG+      ++D R SG   G  I H +PEAA+GG + LV
Sbjct: 485 GGPGMQE---MLYPTSYLKSKGLGKACALVTDGRFSGGTSGLSIGHASPEAAQGGAIGLV 541

Query: 505 ENGDLIEVDIPNRTLHLHVSDEELARRRAA 534
           ++GD IE+DIPNR ++L +SDEEL RRR A
Sbjct: 542 QDGDRIEIDIPNRKINLALSDEELQRRRDA 571


Lambda     K      H
   0.318    0.135    0.402 

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: 947
Number of extensions: 54
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 579
Length of database: 621
Length adjustment: 37
Effective length of query: 542
Effective length of database: 584
Effective search space:   316528
Effective search space used:   316528
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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