GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proP in Pseudomonas stutzeri RCH2

Align proline porter II (characterized)
to candidate GFF1547 Psest_1584 Arabinose efflux permease

Query= CharProtDB::CH_024324
         (500 letters)



>FitnessBrowser__psRCH2:GFF1547
          Length = 452

 Score =  255 bits (652), Expect = 2e-72
 Identities = 134/413 (32%), Positives = 230/413 (55%), Gaps = 14/413 (3%)

Query: 24  RKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGG 83
           +  + AA +GNA+EW+DF V+GF+A  + ++FFP       ++ A ATF V F +RP+GG
Sbjct: 10  KNQVLAAVIGNALEWYDFIVFGFLAVVISRLFFPAESEYSALLMATATFGVGFFMRPIGG 69

Query: 84  LFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGG 143
           +  G+  D+ GR+  L + I +M++S   I   P +  IGI AP+L+++ ++ QGF+ GG
Sbjct: 70  VLLGIYADRKGRKAALQLIISLMTLSIAMIAFAPPFAAIGIAAPLLIVLARLMQGFATGG 129

Query: 144 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIP 203
           E+  A+ F+ E +P  +RG  GSW  FG       GAGV  L+++ +   +   WGWRIP
Sbjct: 130 EFASATSFLIESAPANRRGLYGSWQMFGQGLAVFCGAGVTALVTSNLSPEDLDSWGWRIP 189

Query: 204 FFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLLT 263
           F I L +G +GL++R  L ET AF +      Q  +E      K S   +   + R ++T
Sbjct: 190 FIIGLIIGPVGLWMRRNLSETEAFLE----ARQAPKE------KQSLARMLRSHLRQVVT 239

Query: 264 CIGLVIATNVTYYMLLTYMPSYLSHNLHYS-EDHGVLIIIAIMIGMLFVQPVMGLLSDRF 322
            + L +   V +Y++L YMP++ +  L    +D     ++A+ + +  + PV G LSDR 
Sbjct: 240 VMALTVCGTVAFYVILVYMPTFANRQLGMQLKDAFTAQVVAVAV-LTLLMPVFGALSDRV 298

Query: 323 GRRPFVLLGSVALFVLAIPAFILIN-SNVIGLIFAGLLMLAVILNCFTGVMASTLPAMFP 381
           GR+  +++ ++ L V   P F  I+ +   G +    L+L  +L  F G  ++ +   FP
Sbjct: 299 GRKLLMIVATLGLLVALYPLFSWIHAAPSFGRLLTMQLILCSLLAVFFGPFSAAVAEQFP 358

Query: 382 THIRYSALAAAFNISVLV-AGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGLI 433
             +R + LA A+N++V++  G    +  WL++++   + P +Y++    +GLI
Sbjct: 359 AGVRSTGLALAYNLAVMIFGGFAQFIVTWLIQNTGMAIAPVFYVLFAVTLGLI 411


Lambda     K      H
   0.327    0.142    0.429 

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: 604
Number of extensions: 36
Number of successful extensions: 6
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: 500
Length of database: 452
Length adjustment: 33
Effective length of query: 467
Effective length of database: 419
Effective search space:   195673
Effective search space used:   195673
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: 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