GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS06245 BWI76_RS06245
           proline-specific permease ProY
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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