GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proY in Escherichia coli BW25113

Align Proline-specific permease (ProY) (characterized)
to candidate 14712 b0576 phenylalanine transporter (NCBI)

Query= TCDB::P37460
         (456 letters)



>lcl|FitnessBrowser__Keio:14712 b0576 phenylalanine transporter
           (NCBI)
          Length = 458

 Score =  396 bits (1017), Expect = e-115
 Identities = 204/447 (45%), Positives = 292/447 (65%), Gaps = 11/447 (2%)

Query: 7   LKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRALGEMS 66
           L RGL  RHI+ +ALG AIGTGLF G   AI+MAGP+VLL Y + G+ A++IMR LGEM 
Sbjct: 19  LHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMRQLGEMV 78

Query: 67  VHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAVPHWIW 126
           V  P + SF+ +A +  GP AG+++GW Y    ++V +A++TA GIYM  WFP VP WIW
Sbjct: 79  VEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPDVPTWIW 138

Query: 127 VLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQPTGIHN 186
             +  +II A+NL++V+++GE EFWF+  KV  II MI  G G+ +   G+GG+   I N
Sbjct: 139 AAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMI--GFGLWLLFSGHGGEKASIDN 196

Query: 187 LWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILVF 246
           LW  GGFF+ GW G+I+SL ++MF++GG+E+IGITA EA+DPEKSIP+A+N V  RIL+F
Sbjct: 197 LWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQVVYRILLF 256

Query: 247 YVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDVFGVG 306
           Y+G+L V++++YPW +V +N SPFV+ F ++     AS LNFV+L ASLS  NS V+   
Sbjct: 257 YIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYNSGVYSNS 316

Query: 307 RMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVIASLATF 366
           RML G++ QG+APK   + SRRG+P  ++++        V +NY++P+  F ++ +L   
Sbjct: 317 RMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLLPQKAFGLLMALVVA 376

Query: 367 ATVWVWIMILLSQIAF----RRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIGYH 422
             +  WIMI L+ + F    RR+    + KAL +  P G    IA   FL  I+ L+   
Sbjct: 377 TLLLNWIMICLAHLRFRAAMRRQGRETQFKALLY--PFGNYLCIA---FLGMILLLMCTM 431

Query: 423 PDTRISLYVGFAWIVLLLIGWIFKRRR 449
            D R+S  +   WIV L + +   RR+
Sbjct: 432 DDMRLSAILLPVWIVFLFMAFKTLRRK 458


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: 658
Number of extensions: 34
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: 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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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