GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Escherichia coli BW25113

Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate 14540 b0402 predicted cryptic proline transporter (NCBI)

Query= TCDB::P24207
         (458 letters)



>FitnessBrowser__Keio:14540
          Length = 457

 Score =  395 bits (1014), Expect = e-114
 Identities = 201/446 (45%), Positives = 288/446 (64%), Gaps = 11/446 (2%)

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

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

Query: 139 AAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMI--GFGLWLLFSGHGGEKASIDN 196
             +  +II AVNL++V+++GE EFWF+  KV  II MI  GFG+ +   G+GG+   I N
Sbjct: 127 VLSVVLIICAVNLMSVKVFGELEFWFSFFKVATIIIMIVAGFGIIIWGIGNGGQPTGIHN 186

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

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

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

Query: 377 TLLLNWIMICLAHLRFRAAMRRQGRETQFKALLYPFGNYLCIAFLGMILLLMCT-----M 431
             +  WIMI L+ + F    RR+    + KAL +     +     G+I LL         
Sbjct: 367 ATVWVWIMILLSQIAF----RRRLPPEEVKALKFKVPGGVATTIGGLIFLLFIIGLIGYH 422

Query: 432 DDMRLSAILLPVWIVFLFMAFKTLRR 457
            D R+S  +   WIV L + +   RR
Sbjct: 423 PDTRISLYVGFAWIVVLLIGWMFKRR 448


Lambda     K      H
   0.329    0.143    0.447 

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: 654
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: 458
Length of database: 457
Length adjustment: 33
Effective length of query: 425
Effective length of database: 424
Effective search space:   180200
Effective search space used:   180200
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 (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:

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