GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocE in Klebsiella michiganensis M5al

Align Amino-acid permease RocE (characterized)
to candidate BWI76_RS06245 BWI76_RS06245 proline-specific permease ProY

Query= SwissProt::P39137
         (467 letters)



>FitnessBrowser__Koxy:BWI76_RS06245
          Length = 456

 Score =  302 bits (774), Expect = 1e-86
 Identities = 162/445 (36%), Positives = 252/445 (56%), Gaps = 6/445 (1%)

Query: 6   DNGNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTML 65
           ++ N+L+R + +RH+  ++LG  IGTG F G+   I  AGP   +L+Y++GG   ++ M 
Sbjct: 2   ESSNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGP-SVLLAYIIGGVAAYIIMR 60

Query: 66  CLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPH 125
            LGE++V  P + SF  YA  ++ P  G+  GW Y     +    +  + G  M  WFP 
Sbjct: 61  ALGEMSVHNPAASSFSRYAQDYLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPA 120

Query: 126 IDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILG-GAAMFGLIDLKG 184
           +  W+W L    ++  +N ++ K F E EFWFS  K+  I++ I+ G G  ++G+ +  G
Sbjct: 121 VPHWVWVLSVVLIICAVNLMSVKVFGELEFWFSFFKVATIIIMILAGFGIIIWGIGN--G 178

Query: 185 GEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQ 244
           G+       +   G F NG   M++++  V FA+ G E+IG+ AGE++DPEK+IPR+I  
Sbjct: 179 GQPTGIHNLWSNGGFFSNGWLGMVMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINS 238

Query: 245 TVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVA 304
              R LVF+V ++ VI  + PW Q G   SPFV  F+ +GI +AA I+NFV+L A LS  
Sbjct: 239 VPMRILVFYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHLGITFAASILNFVVLTASLSAI 298

Query: 305 NSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYM 364
           NS ++   R+L+ MA +G A K   KT++RGVP  +++V       ++   +   E V++
Sbjct: 299 NSDVFGVGRMLHGMAEQGSAPKMFAKTSRRGVPWVTVMVMTIALLFAVYLNYIMPENVFL 358

Query: 365 VLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVL 424
           V+ SLA  +    WI I LSQI FRR+   E  K   LKFK P      +IGL     ++
Sbjct: 359 VIASLATFATVWVWIMILLSQIAFRRRLPPEEAKA--LKFKVPGGVTTTVIGLLFLVFII 416

Query: 425 ISLAFDPEQRIALYCGVPFMIICYI 449
             + + P+ RI+LY G  ++I+  I
Sbjct: 417 GLIGYHPDTRISLYVGFAWIILLLI 441


Lambda     K      H
   0.329    0.142    0.438 

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: 583
Number of extensions: 23
Number of successful extensions: 4
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: 467
Length of database: 456
Length adjustment: 33
Effective length of query: 434
Effective length of database: 423
Effective search space:   183582
Effective search space used:   183582
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