GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gci in Azospirillum brasilense Sp245

Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate AZOBR_RS26635 AZOBR_RS26635 mandelate racemase

Query= BRENDA::A9CEQ8
         (378 letters)



>FitnessBrowser__azobra:AZOBR_RS26635
          Length = 393

 Score =  288 bits (738), Expect = 1e-82
 Identities = 162/386 (41%), Positives = 223/386 (57%), Gaps = 13/386 (3%)

Query: 1   MKITAVRTHLLEHRLDTP-FESASMRFDRRAHVLVEIECDDGTVGWGEC--LGPARP-NA 56
           M I  + T +L+  L+   F S+   F  R  +LV I  DDG VGWGE    GPA P  +
Sbjct: 1   MLIKKIDTFVLKTPLNAKTFYSSQAAFPERNSLLVRITTDDGLVGWGEGGQYGPAEPPES 60

Query: 57  AVVQAYSGWLIGQDPRQTEKIWAVLYNALRDQGQRGLSLTALSGIDIALWDIKGKHYGAS 116
            ++   +  LIG+   Q  +++  LY+  RD GQ+G  + ALS IDIALWD+ GK     
Sbjct: 61  CIIDVLAPRLIGRRADQPVRVFEDLYSFCRDFGQKGTYIEALSAIDIALWDLWGKSLNRP 120

Query: 117 ISMLLGGRWRESVRAYATGSFKRD---NVDRVSDNASEMAER-RAEGFHACKIKIGF-GV 171
           +  L+GG +R+ V AY TG +  D   +  R+    +E A+R R  G  A KIKIG   +
Sbjct: 121 VHALMGGAFRDKVAAYGTGCYYPDYFRDTPRMMAALAEEAQRYREAGLPAIKIKIGLLPI 180

Query: 172 EEDLRVIAAVREAIGPDMRLMIDANHGYTVTEAITLGDRAAGFGIDWFEEPVVPEQLDAY 231
            +D+  +A VR+ +GPD  +M+DANH Y    AI +G     F + WFEEPV PE    Y
Sbjct: 181 AQDIERVALVRDVLGPDTLIMVDANHAYNTAGAIRIGRALERFDVRWFEEPVPPEDRQGY 240

Query: 232 ARVRAGQPIPVAGGETWHGRYGMWQALSAGAVDILQPDLCGCGGFSEIQKIATLATLHGV 291
            RVR    +P+AGGE  + RYG  + L+ G +DI QPDLC  GGF+E QKI  L T HGV
Sbjct: 241 RRVRDSIDVPIAGGECEYTRYGFRELLAGGCIDIAQPDLCCAGGFTEWQKILALTTAHGV 300

Query: 292 RIVPHVWGTGVQIAAALQFMAAMTPDPVRVNPI----EPIMEFDRTHNPFRQAVLREPLE 347
             VPH+WG+G+ +AAALQ +A     P     +    EP++EFDRTHNP R  +L +   
Sbjct: 301 MTVPHIWGSGIALAAALQALATAPLVPYTALGVPLQNEPMVEFDRTHNPLRDDLLIDNFT 360

Query: 348 AVNGVVTIPDGPGLGIEINRDALTEF 373
            V+G + +P G GLG+E++ D L  +
Sbjct: 361 LVDGCLALPGGAGLGVEVDPDQLARY 386


Lambda     K      H
   0.321    0.138    0.431 

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: 496
Number of extensions: 24
Number of successful extensions: 5
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: 378
Length of database: 393
Length adjustment: 30
Effective length of query: 348
Effective length of database: 363
Effective search space:   126324
Effective search space used:   126324
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 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:

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:

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:

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:

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