GapMind for catabolism of small carbon sources

 

Alignments for a candidate for CAT in Burkholderia phytofirmans PsJN

Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate BPHYT_RS33230 BPHYT_RS33230 amino acid permease

Query= TCDB::ALD51314.1
         (582 letters)



>FitnessBrowser__BFirm:BPHYT_RS33230
          Length = 486

 Score =  256 bits (655), Expect = 1e-72
 Identities = 147/438 (33%), Positives = 240/438 (54%), Gaps = 21/438 (4%)

Query: 44  ARSGGDMKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSA 103
           A  G  + +SL    +   G+G ++GAG+FV +G A++  AGP++VLS+ + G       
Sbjct: 21  ADEGHSLSKSLGAISITAMGIGAIIGAGIFVLTGTAAAQFAGPSIVLSFVLGGIACAFVG 80

Query: 104 FCYTEFAVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGYLCTAL- 162
            CY+E A  +PV G +++Y   T GE  A++ G +LI++Y +  A VA  ++GY+ + L 
Sbjct: 81  LCYSELAAMLPVCGSSYTYTYATLGEIFAWIIGWDLILEYAMGAATVAVGWSGYIVSLLH 140

Query: 163 --GIE-----SKLRITVNGLPDGFNEIDVV---AVLVVLALTVIICYSTRESSVLNMVLT 212
             GI      +    TV  L DG     +V   A++++  LT ++   T+ES+ LN ++ 
Sbjct: 141 NVGISIPPVLATAPGTVIKLADGTTATGIVNLPAIVIIAILTTMLVLGTKESARLNNIMV 200

Query: 213 VLHIVFIVFVIVIGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYDAV 272
            + +V +V  I +G       N+     +N    F  FG SG+  G+A+V+ ++IG+DAV
Sbjct: 201 AVKLVVVVAFIALGVFFIKPANWHPFIPAN-TGEFGNFGMSGILRGSAVVFFAFIGFDAV 259

Query: 273 STMAEEVKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAFMGSDG 332
           ST A+E K P +D+P+G+ GS+I+ T+LY L+A  ++ L+PY  ++   P +   + + G
Sbjct: 260 STAAQEAKKPQRDMPIGILGSLIICTILYILVAGVLTGLVPYAELNVPDPIAKG-VDAIG 318

Query: 333 WRWVSNVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAF 392
             W S +I +GA  G+ T +LV + GQ+R    +    ++P  FA+VHP+  TP  +   
Sbjct: 319 LNWFSILIKIGALTGLTTVILVLLYGQSRIFFTMSTDGLLPPLFARVHPRLQTPYLSQIL 378

Query: 393 LGICTAAIALFTDLQILLNLVSIGTLFVFYMVANAVIYKRYVSVGVTNPW--------PT 444
           +G   A +A  T + +L  +VSIGTLF F +V  AVIY R      + P+        P 
Sbjct: 379 IGSVVAIVAALTPISVLGEMVSIGTLFAFILVCGAVIYLRRSDSDASRPFRVPGVPVVPV 438

Query: 445 LSYLFCFSLTSILFTLLW 462
           L  LFC  L + L  + W
Sbjct: 439 LGILFCLLLMAGLPLVTW 456


Lambda     K      H
   0.326    0.139    0.423 

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: 714
Number of extensions: 40
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: 582
Length of database: 486
Length adjustment: 35
Effective length of query: 547
Effective length of database: 451
Effective search space:   246697
Effective search space used:   246697
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 (21.7 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