GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Marinobacter adhaerens HP15

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF3114 HP15_3057 leucine/isoleucine/valine transporter permease subunit

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__Marino:GFF3114
          Length = 423

 Score =  338 bits (868), Expect = 2e-97
 Identities = 179/305 (58%), Positives = 221/305 (72%), Gaps = 18/305 (5%)

Query: 142 ILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAAL 201
           +LIY+MLA GLN+VVGLAGLLDLGYVAFYAVGAY++ALLS Y G+SFW+ LP+  + AAL
Sbjct: 122 VLIYIMLALGLNVVVGLAGLLDLGYVAFYAVGAYTFALLSQYTGISFWLALPIGALLAAL 181

Query: 202 WGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLFGIPF-- 259
           +G++LGFPVLRLRGDYLAIVTL FGEIIR++L NWT +T G  GI  IP  TLFG+ F  
Sbjct: 182 FGLVLGFPVLRLRGDYLAIVTLGFGEIIRILLNNWTTLTGGPNGIGGIPDPTLFGMEFGR 241

Query: 260 ---DATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALRED 316
              +     F + F +  S  +  IFL+ + L L + TA V  R  RMP+GRAWEALRED
Sbjct: 242 RVKEEGNTSFHETFGIAYSGEHKVIFLYLIALVLAVFTALVIRRFMRMPVGRAWEALRED 301

Query: 317 EIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLG 376
           EIA RSLG++    KL+AF  GA FAGFAG+ FA++QGF+SPESFVFLESA+ILAIVVLG
Sbjct: 302 EIAARSLGLSRTAVKLSAFTIGAFFAGFAGTVFASKQGFISPESFVFLESAIILAIVVLG 361

Query: 377 GMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVMLFKPRG 436
           GMGS  G+ +AAI +    EL RE S              YRMLIFG AMV++M+++P+G
Sbjct: 362 GMGSQIGVVLAAIAVTILPELAREFS-------------EYRMLIFGAAMVLMMVWRPQG 408

Query: 437 FVGSR 441
            +  R
Sbjct: 409 LMPMR 413


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: 638
Number of extensions: 41
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: 423
Length adjustment: 32
Effective length of query: 431
Effective length of database: 391
Effective search space:   168521
Effective search space used:   168521
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: 51 (24.3 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