Alignments for a candidate for xad in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for xad in Azospirillum brasilense Sp245

Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate AZOBR_RS15015 AZOBR_RS15015 dihydroxy-acid dehydratase

Query= BRENDA::P39358
         (655 letters)



>FitnessBrowser__azobra:AZOBR_RS15015
          Length = 621

 Score =  201 bits (512), Expect = 6e-56
 Identities = 194/634 (30%), Positives = 305/634 (48%), Gaps = 95/634 (14%)

Query: 72  GLRGAD-GKPVALALHQ------GHYEL-DIQMKAAAEVIKANH-ALPYAVYVSDPCDGR 122
           G++  D GKP+    +       GH  L D+    A E+ KA   A  +     D  DG 
Sbjct: 26  GMKDGDFGKPIIAIANSFTQFVPGHVHLKDLGQLVAREIEKAGGVAKEFNTIAVD--DGI 83

Query: 123 TQGTTGMFDSLPYRNDASMVMRRLIRSLPDAKAVIGVASCDKGLPATMMALAAQHNIATV 182
             G  GM  SLP R   +  +  ++ +   A A++ +++CDK  P  +MA A + NI  V
Sbjct: 84  AMGHDGMLYSLPSRELIADAVEYMVNA-HCADALVCISNCDKITPGMLMA-AMRLNIPAV 141

Query: 183 LVPGGATLPAKDGEDNGKVQT-----IGARFANGELSLQDAR-----RAGCKACASSGGG 232
            V GG   P + G+ N + +T     I A  A  + ++ D       R  C  C    G 
Sbjct: 142 FVSGG---PMEAGKVNWRGKTKAVDLIDAMVAAADPTVSDEEAAVMERGSCPTC----GS 194

Query: 233 CQFLGTAGTSQVVAEGLGLAIPHSALAPSGEPVWREIARASARAALNLSQKGITT----- 287
           C  + TA +   + E LGL++P +    +     +E+  A+ R A+ L ++         
Sbjct: 195 CSGMFTANSMNCLTEALGLSLPGNGTILATHADRKELFLAAGRMAVELCRRWYQEEDATA 254

Query: 288 --REILTDKAIENAMTVHAAFGGSTNLLLHIPAIAHQAGCHIP-TVDDWIRINKRVPRLV 344
             R I T +A ENAMT+  A GGSTN +LH+ A A +    +P T+ D  R+++RVP + 
Sbjct: 255 LPRGIATFEAFENAMTLDIAMGGSTNTVLHLLAAAQEG--QVPFTMADIDRLSRRVPNVC 312

Query: 345 SVLPNGPVYHPTVNAFMAGGVPEVMLHLRSLGLLHEDVMTVTGSTLKENLDWWE------ 398
            V P     H   +   AGG+  ++  L   GLL+ DV TV   TL + LD W+      
Sbjct: 313 KVAPAVSDVH-IEDVHKAGGIFGILGELDRGGLLNRDVATVHAKTLGDALDRWDVKRTQD 371

Query: 399 ---HS---------------ERRQRFKQLLLDQEQINADEVIMSPQQAKARGLTSTITFP 440
              H+                + +R+ +L LD+++     VI S   A ++     + F 
Sbjct: 372 EGVHTMFKAAPGGIPTTIAFSQEKRWPELDLDRDK----GVIRSVDSAFSKDGGLAVLF- 426

Query: 441 VGNIAPEGSVIKSTAIDPSMIDEQGIYYHKGVAKVYLSEKSAIYDIKHDKIKAGDILVII 500
            GNIA +G ++K+  +D S +         G A+V+ S+ +A+  I  D +KAGD++VI 
Sbjct: 427 -GNIAEKGCIVKTAGVDASNL------VFAGPARVFESQDAAVEAILGDTVKAGDVVVIR 479

Query: 501 GVGP-SGTGMEETYQVTSALKHLSYGKHVSLITDARFSGVSTGACIGHVGPEALAGGPIG 559
             GP  G GM+E    TS LK    GK  +L+TD RFSG ++G  IGH  PEA  GG IG
Sbjct: 480 YEGPRGGPGMQEMLYPTSYLKSKGLGKACALVTDGRFSGGTSGLSIGHASPEAAQGGAIG 539

Query: 560 KLRTGDLIEIKIDCRELHGEVNFLGTRSDEQLPSQEEATAILNA---RPSHQDLLPDPEL 616
            ++ GD IEI I  R+++  +      SDE+L  + +A     A   +P++++ +  P L
Sbjct: 540 LVQDGDRIEIDIPNRKINLAL------SDEELQRRRDAENAKGADAWKPANRNRVVSPAL 593

Query: 617 PDDTRLWAMLQAVSGGTWTGCIYDVNKI-GAALR 649
               R +A   A++     G + DV+++ G A++
Sbjct: 594 ----RAYA---ALTTSADRGAVRDVSQVEGIAMK 620


Lambda     K      H
   0.317    0.135    0.400 

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: 974
Number of extensions: 50
Number of successful extensions: 6
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: 655
Length of database: 621
Length adjustment: 38
Effective length of query: 617
Effective length of database: 583
Effective search space:   359711
Effective search space used:   359711
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: 54 (25.4 bits)

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

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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, or view the source code.

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