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_RS08240 AZOBR_RS08240 ABC transporter permease

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__azobra:AZOBR_RS08240
          Length = 505

 Score =  380 bits (976), Expect = e-110
 Identities = 213/401 (53%), Positives = 268/401 (66%), Gaps = 31/401 (7%)

Query: 58  LLAIFVAVAAIGRFAMVVFIRPNIDRRKLSKA-REGELD-ISTEKSFFHRHFLKIALIAL 115
           L  I +A  A+     V+ IR    R KLS+A R+  +D I+ +     R    IA++  
Sbjct: 102 LRVILIAGGAVIAIRAVLAIRTG--RSKLSQAERDKRMDHIAAQVQHASRWLGPIAVVVA 159

Query: 116 LLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAY 175
           L +P   +A +        + + GI +L Y+ML WGLNIVVGLAGLLDLGYVAFYAVGAY
Sbjct: 160 LAFPFTPLADR-------QLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAY 212

Query: 176 SYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLIN 235
           SYALL+ YFG SFWV LPL+G  AA+ GV+LGFPVLRLRGDY AIVTL FGEIIR++LIN
Sbjct: 213 SYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILIN 272

Query: 236 WTDVTKGTFGISSIPKATLFGI------PFDATAGGFAKLFHLPISSAYYKIFLFYLILA 289
           W   T G  GIS IP+ + FGI      P + TA  F ++F L  S  +  IFL+YLIL 
Sbjct: 273 WYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTA-AFHEMFGLEFSPLHRIIFLYYLILV 331

Query: 290 LCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFF 349
           L ++    T+R+R++P+GRAWEALRED+IAC SLGIN    KL AFA  AMF GFAGSFF
Sbjct: 332 LALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFF 391

Query: 350 AARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFG 409
           A RQGF+SPESF F+ESA+ILAIVVLGGMGS  G+ +AA +++G  E  RE++       
Sbjct: 392 ATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELAD------ 445

Query: 410 PDFTPELYRMLIFGLAMVVVMLFKPRGFVGSREPTAFLRER 450
                  YRML FG+ MV++ML++PRG +  R+PT  L  R
Sbjct: 446 -------YRMLAFGMGMVLIMLWRPRGLLAHRDPTILLHGR 479


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: 754
Number of extensions: 49
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: 505
Length adjustment: 34
Effective length of query: 429
Effective length of database: 471
Effective search space:   202059
Effective search space used:   202059
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: 52 (24.6 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