GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proP in Klebsiella michiganensis M5al

Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate BWI76_RS26735 BWI76_RS26735 MFS transporter

Query= SwissProt::Q47421
         (501 letters)



>FitnessBrowser__Koxy:BWI76_RS26735
          Length = 440

 Score =  253 bits (645), Expect = 1e-71
 Identities = 146/429 (34%), Positives = 236/429 (55%), Gaps = 17/429 (3%)

Query: 26  KAITAAALGNAMEWFDFGVYGFVAYAL-GQVFFPGADPGVQMIAALATFSVPFLIRPLGG 84
           K + A+ +G A+E+FDF +Y   A  +   +FFP  DP    + +LATF++ F+ RP+G 
Sbjct: 22  KVVVASLIGTAIEFFDFYIYATAAVIVFPHIFFPQGDPAAATLQSLATFAIAFIARPIGS 81

Query: 85  VFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSVGG 144
             FG  GD+ GR+  L  +++ M IST  IGL+P YE IGI AP+LL LA+  QG  +GG
Sbjct: 82  AVFGHFGDRVGRKTTLVASLLTMGISTVVIGLLPGYETIGIMAPVLLALARFGQGLGLGG 141

Query: 145 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWRLP 204
           E+ GA++   E +P RKR   GS+   G+  GF    G  +L+S L+ +Q F+ WGWR+P
Sbjct: 142 EWGGAALLATENAPPRKRALYGSFPQLGAPIGFFFANGTFLLLSWLLTDQQFMEWGWRMP 201

Query: 205 FFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKSLLV 264
           F  +  L +IGLY+R +L E+P F +     +Q           +    + T H +  ++
Sbjct: 202 FIFSAVLVIIGLYVRVSLHESPVFAKVAAAKKQ---------VKIPLGTLLTKHVRVTVL 252

Query: 265 CIGLVIATNVTYYMLLTYMPSYLSHS----LHYSENHGVLIIIAIMIGMLFVQPVMGLLS 320
              +++AT   +Y++  Y  ++ + +    L    N  + +++  +IG   + PV GLL+
Sbjct: 253 GTFIMLATYTLFYIMTVYSMTFSTAAAPIGLGLPRNEVLWMLMMAVIGFGVMVPVAGLLA 312

Query: 321 DRFG-RKPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLAVILNAFTGVMASTLPA 379
           D FG RK  VVI ++ + F       L+ S    L+F  LL+   ++    G M + LP 
Sbjct: 313 DAFGRRKSMVVITTLIILFALFAFKPLLGSGNPLLVFAFLLIGLSLMGLTFGPMGALLPE 372

Query: 380 LFPTHIRYSALASAFNI-SVLIAGLTPTVAAWLVESSQNLYMPAYYLMVIAVIGLLTGLF 438
           LFPT +RY+  + ++N+ S+L A + P +AAWL + +  L     YL  +A + ++  L 
Sbjct: 373 LFPTEVRYTGASFSYNVSSILGASVAPYIAAWL-QGNYGLPAVGLYLAAMAALTMIALLL 431

Query: 439 MKETANKPL 447
             ET ++ L
Sbjct: 432 THETRHQSL 440


Lambda     K      H
   0.327    0.142    0.427 

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: 536
Number of extensions: 24
Number of successful extensions: 5
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: 501
Length of database: 440
Length adjustment: 33
Effective length of query: 468
Effective length of database: 407
Effective search space:   190476
Effective search space used:   190476
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