GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Azospirillum brasilense Sp245

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AZOBR_RS32410 AZOBR_RS32410 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__azobra:AZOBR_RS32410
          Length = 355

 Score =  205 bits (521), Expect = 2e-57
 Identities = 122/344 (35%), Positives = 178/344 (51%), Gaps = 33/344 (9%)

Query: 105 RHFLKIALIALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDL 164
           R F    L+  + +  V  AI G   S  Y+    I  +I+V+L+  LN V G AGLL +
Sbjct: 26  RRFAWTLLLLAVAFGAVPAAIVGTGSS--YLAQIAITTMIFVILSASLNHVTGTAGLLSI 83

Query: 165 GYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLA 224
           G+ AFY +GAY+ ALLS+  GL F V LP +G+ AAL+G ++  P +RL   Y A+ TL 
Sbjct: 84  GHAAFYGIGAYAAALLSTKLGLPFIVTLPAAGLIAALFGFLVALPTMRLVSIYFAVATLG 143

Query: 225 FGEIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLF 284
            GE+I +VL+NW DVT+G  GI  IP   LFG   D                    +  +
Sbjct: 144 IGEMIYVVLLNWVDVTRGPMGIRGIPPIELFGWQADTL------------------LTRY 185

Query: 285 YLILALCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGF 344
             +  + +   +V  RL     G A  ALRED+    S+GIN    K+ +F     FAG 
Sbjct: 186 LAVAVIAVACVWVLHRLTHSYYGNALRALREDDQCADSMGINVERLKIESFVVATFFAGI 245

Query: 345 AGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFL 404
           AG+  A    +++P++F F+ES +ILA+VV+GG+GSL G  + A+ M+   E LR++   
Sbjct: 246 AGALLAHTSAYIAPDNFRFMESILILAMVVVGGLGSLPGAVVGALFMIVLPEALRDIGD- 304

Query: 405 KLIFGPDFTPELYRMLIFGLAMVVVMLFKPRGFVGSREPTAFLR 448
                       YRM+  G  M + +L  P+G +       F+R
Sbjct: 305 ------------YRMIAVGATMFLSILLLPKGMLAEGTALGFVR 336


Lambda     K      H
   0.330    0.145    0.432 

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: 478
Number of extensions: 27
Number of successful extensions: 3
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: 463
Length of database: 355
Length adjustment: 31
Effective length of query: 432
Effective length of database: 324
Effective search space:   139968
Effective search space used:   139968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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