GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Azospirillum brasilense Sp245

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate AZOBR_RS24710 AZOBR_RS24710 ABC transporter ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__azobra:AZOBR_RS24710
          Length = 360

 Score =  200 bits (508), Expect = 6e-56
 Identities = 106/259 (40%), Positives = 162/259 (62%), Gaps = 5/259 (1%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M+ IR++NL K F        A+  + + + +G    +LGPSG GK+T L+L+AG E PT
Sbjct: 1   MSGIRIKNLRKSFGT----YTALHGIDLQVPNGTLLALLGPSGCGKSTTLQLLAGFEAPT 56

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
            G I+ D+  +SS R V+  PEKRGI++VFQN+A++P+ TV +N+AF L + ++PK +I 
Sbjct: 57  EGEIWADDVLLSSARGVL-PPEKRGISLVFQNYAVWPHKTVAENVAFGLAIRRLPKAEIA 115

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
            ++      + L  + +RYP ELSGGQ QR A+ARAL  +P++LLLDEP SNLDA +RE 
Sbjct: 116 ERLDRTLRTVRLEALRDRYPSELSGGQQQRVALARALAVEPRILLLDEPLSNLDAHLREE 175

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
            R  +R++     LTT+ V+HD ++    A++  V+ +G   Q+G+P +I+E P+   +A
Sbjct: 176 MRFEIRQVHDLLGLTTVYVTHDQSEALVTADRIAVMKSGHLQQLGSPEDIFERPSNAFVA 235

Query: 241 RLTGEINLIQAKIIENNAI 259
              G  N +      N AI
Sbjct: 236 TFIGANNELAGTSEGNGAI 254


Lambda     K      H
   0.317    0.136    0.374 

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: 283
Number of extensions: 11
Number of successful extensions: 2
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: 371
Length of database: 360
Length adjustment: 30
Effective length of query: 341
Effective length of database: 330
Effective search space:   112530
Effective search space used:   112530
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 (21.6 bits)
S2: 49 (23.5 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