GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proY in Klebsiella michiganensis M5al

Align Proline-specific permease (ProY) (characterized)
to candidate BWI76_RS07360 BWI76_RS07360 phenylalanine transporter

Query= TCDB::P37460
         (456 letters)



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

 Score =  395 bits (1014), Expect = e-114
 Identities = 200/447 (44%), Positives = 288/447 (64%), Gaps = 3/447 (0%)

Query: 2   ESNNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRA 61
           ES   L RGL  RHI+ +ALG AIGTGLF G   AI+MAGP+VLL Y + G+ A++IMR 
Sbjct: 13  ESGPTLHRGLQNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYAVAGIVAFLIMRQ 72

Query: 62  LGEMSVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAV 121
           LGEM V  P + SF+ +A +  GP AG+++GW Y    ++V +A++TA GIYM  W P V
Sbjct: 73  LGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWLPDV 132

Query: 122 PHWIWVLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQP 181
           P WIW  +  LII A+NL++V+++GE EFWF+  KV  II MI  G G+ +   G+GG  
Sbjct: 133 PTWIWAAAFFLIINAVNLVNVRLYGEAEFWFALIKVLAIIGMI--GFGLWMLFGGHGGSK 190

Query: 182 TGIHNLWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPM 241
            GI NLW +GGFF+ GW G+IMSL ++MF++GG+E+IGITA EA++PEKSIP+A+N V  
Sbjct: 191 AGIDNLWKHGGFFATGWHGLIMSLAVIMFSFGGLELIGITAAEAQNPEKSIPKAVNQVVY 250

Query: 242 RILVFYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINSD 301
           RIL+FY+G+L V++++YPW ++ ++ SPFV+ F ++     AS LNFV+L ASLS  NS 
Sbjct: 251 RILLFYIGSLVVLLALYPWVEIQSDSSPFVMIFHNLDSNVVASALNFVILVASLSVYNSG 310

Query: 302 VFGVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVIA 361
           V+   RML G++ QG+APK  A+ S+RG+P  ++L+  I     V LNY++P+    ++ 
Sbjct: 311 VYSNSRMLFGLSVQGNAPKFLARVSKRGVPVNSLLLSGIITSLVVVLNYLLPQKALGLLM 370

Query: 362 SLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIGY 421
           +L     +  WIMI L+ + F R     + +  KFK      +    + FL  I+ L+  
Sbjct: 371 ALVVATLLLNWIMICLAHLKF-RAAQRRKGREPKFKALLSPASNYICIAFLALILVLMCT 429

Query: 422 HPDTRISLYVGFAWIVLLLIGWIFKRR 448
               R+S  +   WI+ L   +   RR
Sbjct: 430 IDGMRLSAILLPVWILFLFAAFKTLRR 456


Lambda     K      H
   0.329    0.143    0.449 

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: 666
Number of extensions: 37
Number of successful extensions: 2
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: 456
Length of database: 458
Length adjustment: 33
Effective length of query: 423
Effective length of database: 425
Effective search space:   179775
Effective search space used:   179775
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