GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__azobra:AZOBR_RS08240 AZOBR_RS08240 ABC
           transporter permease
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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