GapMind for catabolism of small carbon sources

 

Alignments for a candidate for permease in Escherichia coli BW25113

Align histidine permease (characterized)
to candidate 14712 b0576 phenylalanine transporter (NCBI)

Query= reanno::pseudo3_N2E3:AO353_12275
         (468 letters)



>FitnessBrowser__Keio:14712
          Length = 458

 Score =  391 bits (1005), Expect = e-113
 Identities = 196/438 (44%), Positives = 278/438 (63%), Gaps = 4/438 (0%)

Query: 8   LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMA 67
           L RGL  RHI+ +ALG AIGTGLF G   AIQMAGPAVLL Y + G   F++MR LGEM 
Sbjct: 19  LHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMRQLGEMV 78

Query: 68  VHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWIW 127
           V  PV+GSF  +A  Y GP AGF+ GW Y    V+VGMA++TA GIYM +WFP+V  WIW
Sbjct: 79  VEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPDVPTWIW 138

Query: 128 VLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTDIS 187
                 I+  +NL NV+++GE EFW +L+KV AI+ MI  GFG+ L   S   G+   I 
Sbjct: 139 AAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMI--GFGLWLL-FSGHGGEKASID 195

Query: 188 NLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRILL 247
           NLW  GGF   G  GLI S AV+MF+FGG+E+IG+TA EA+DP+  +P+A+N V  RILL
Sbjct: 196 NLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQVVYRILL 255

Query: 248 FYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIFGA 307
           FY+ +++VL++++PW ++ S  SPFV IF  L  +  A+ LN V++ A++S  NS ++  
Sbjct: 256 FYIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYNSGVYSN 315

Query: 308 GRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIASIAT 367
            RM+FGL+ QG+APK    +SR GVP  ++++      L VL+NYL+P+  F L+ ++  
Sbjct: 316 SRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLLPQKAFGLLMALVV 375

Query: 368 FATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYFPDT 427
              +  W+MI    +  R +M   Q  + +F    +P+     IAF+  +  ++    D 
Sbjct: 376 ATLLLNWIMICLAHLRFRAAM-RRQGRETQFKALLYPFGNYLCIAFLGMILLLMCTMDDM 434

Query: 428 QAALIVGVVWIVLLVLAY 445
           + + I+  VWIV L +A+
Sbjct: 435 RLSAILLPVWIVFLFMAF 452


Lambda     K      H
   0.329    0.142    0.441 

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: 665
Number of extensions: 31
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: 468
Length of database: 458
Length adjustment: 33
Effective length of query: 435
Effective length of database: 425
Effective search space:   184875
Effective search space used:   184875
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