GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocE in Klebsiella michiganensis M5al

Align arginine permease (characterized)
to candidate BWI76_RS07360 BWI76_RS07360 phenylalanine transporter

Query= CharProtDB::CH_091699
         (590 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS07360 BWI76_RS07360 phenylalanine
           transporter
          Length = 458

 Score =  269 bits (687), Expect = 2e-76
 Identities = 168/479 (35%), Positives = 249/479 (51%), Gaps = 34/479 (7%)

Query: 67  MEDGIGDEDEGEVQNAEVKRELKQRHIGMIALGGTIGTGLFIGLSTPLTNAGPVGALISY 126
           M+D     +  E     + R L+ RHI +IALGG IGTGLF+G+   +  AGP   L+ Y
Sbjct: 1   MKDASTSSETIEESGPTLHRGLQNRHIQLIALGGAIGTGLFLGIGPAIQMAGPA-VLLGY 59

Query: 127 LFMGSLAYSVTQSLGEMATFIPVTSSFTVFSQRFLSPAFGAANGYMYWFSWAITFALELS 186
              G +A+ + + LGEM    PV+ SF  F+ ++  P  G  +G+ YW  + +    EL+
Sbjct: 60  AVAGIVAFLIMRQLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELT 119

Query: 187 VVGQVIQFWTYKVPLAAWISIFWVIITIMNLFPVKYYGEFEFWVASIKVLAIIGFLIYCF 246
             G  +Q+W   VP   W + F++II  +NL  V+ YGE EFW A IKVLAIIG + +  
Sbjct: 120 AAGIYMQYWLPDVPTWIWAAAFFLIINAVNLVNVRLYGEAEFWFALIKVLAIIGMIGFGL 179

Query: 247 CMVCGAGVTGPVGF-RYWRNPGAWGPGIISKDKNEGRFLGWVSSLINAAFTFQGTELVGI 305
            M+ G       G    W++ G +  G          + G + SL    F+F G EL+GI
Sbjct: 180 WMLFGGHGGSKAGIDNLWKHGGFFATG----------WHGLIMSLAVIMFSFGGLELIGI 229

Query: 306 TAGEAANPRKSVPRAIKKVVFRILTFYIGSLLFIGLLVPYNDPKLTQSTSYVSTSPFIIA 365
           TA EA NP KS+P+A+ +VV+RIL FYIGSL+ +  L P+ +    QS S    SPF++ 
Sbjct: 230 TAAEAQNPEKSIPKAVNQVVYRILLFYIGSLVVLLALYPWVE---IQSDS----SPFVMI 282

Query: 366 IENSGTKVLPHIFNAVILTTIISAANSNIYVGSRILFGLSKNKLAPKFLSRTTKGGVPYI 425
             N  + V+    N VIL   +S  NS +Y  SR+LFGLS    APKFL+R +K GVP  
Sbjct: 283 FHNLDSNVVASALNFVILVASLSVYNSGVYSNSRMLFGLSVQGNAPKFLARVSKRGVPVN 342

Query: 426 AVFVTAAFGALAYMETSTGGDKVFEWLLNITGVAGFFAWLFISISHIRFMQALKYRGISR 485
           ++ ++    +L  +       K    L+ +        W+ I ++H++F  A + +G   
Sbjct: 343 SLLLSGIITSLVVVLNYLLPQKALGLLMALVVATLLLNWIMICLAHLKFRAAQRRKG--- 399

Query: 486 DELPFKAKLMPGLAYYAATFMTIIIIIQGFTAFAPKFNGVSFAAAYISIFLFLAVWILF 544
            E  FKA L P   Y    F+ +I+++          +G+  +A      + L VWILF
Sbjct: 400 REPKFKALLSPASNYICIAFLALILVLM------CTIDGMRLSA------ILLPVWILF 446


Lambda     K      H
   0.325    0.140    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: 723
Number of extensions: 33
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: 590
Length of database: 458
Length adjustment: 35
Effective length of query: 555
Effective length of database: 423
Effective search space:   234765
Effective search space used:   234765
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 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