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_RS19685 BWI76_RS19685 lysine transporter

Query= SwissProt::P39137
         (467 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS19685 BWI76_RS19685 lysine
           transporter
          Length = 489

 Score =  376 bits (966), Expect = e-109
 Identities = 187/457 (40%), Positives = 285/457 (62%), Gaps = 18/457 (3%)

Query: 11  LQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGEL 70
           L+R +K+RHL MI++GG IGTG F+ +G TI+QAGP GA+LSY++ G +++  M  LGEL
Sbjct: 13  LRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYILIGLMVYFLMTSLGEL 72

Query: 71  AVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDVWI 130
           A   PVSGSF TY   ++   FGFA GW YW  WAVT A++ ++A  +M  WFP    W+
Sbjct: 73  AAFMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMTYWFPDAPGWV 132

Query: 131 WCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQAPF 190
           W  +F  +MF+LN I+ K F E+E+WFS IK+  +++FII+G   +FG+   KG + A +
Sbjct: 133 WSALFLGIMFLLNWISVKGFGEAEYWFSLIKVATVIIFIIVGVMMIFGI--FKGAQPAGW 190

Query: 191 LTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWRTL 250
                +D  F  G  AM+   + V F+FQGTELIG+AAGESE+PEK IPR+++Q  WR L
Sbjct: 191 SNWVIDDAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESENPEKNIPRAVRQVFWRIL 250

Query: 251 VFFVLSIIVIAGMIPWKQAGVVE--------SPFVAVFEQIGIPYAADIMNFVILIALLS 302
           +F+V +I++I+ +IP+    ++         SPF  VF+  G+  AA IMN VIL A+LS
Sbjct: 251 LFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAIMNAVILTAVLS 310

Query: 303 VANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETV 362
             NSG+YASTR+LY +A +G+A +   K ++ GVP  +L  T  +A L  L+     +TV
Sbjct: 311 AGNSGMYASTRMLYTLACDGKAPRIFSKLSKGGVPRNALYATTVIAGLCFLSSMFGNQTV 370

Query: 363 YMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTV 422
           Y+ LL+ +GM+  + W+ I++S   FRR Y+ +G  + DL +++  +P+ P+    L  +
Sbjct: 371 YLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGNDLNDLPYRSGFFPLGPIFAFVLCLI 430

Query: 423 VLISLAFDPEQR--------IALYCGVPFMIICYIIY 451
           + +   ++   +         A Y G+P  ++ +  Y
Sbjct: 431 ITLGQNYEAFLKDTIDWGGVAATYIGIPLFLVIWFGY 467


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: 676
Number of extensions: 35
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: 467
Length of database: 489
Length adjustment: 34
Effective length of query: 433
Effective length of database: 455
Effective search space:   197015
Effective search space used:   197015
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