GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocE in Escherichia coli BW25113

Align Amino-acid permease RocE (characterized)
to candidate 14398 b0260 putative amino acid/amine transport protein (VIMSS)

Query= SwissProt::P39137
         (467 letters)



>FitnessBrowser__Keio:14398
          Length = 467

 Score =  473 bits (1216), Expect = e-138
 Identities = 219/451 (48%), Positives = 317/451 (70%), Gaps = 1/451 (0%)

Query: 1   MNTNQDNGNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIM 60
           M T Q N   L+RTMK+RHL M+SLGGVIGTG F  TG+ I+  G  G +L+YL+G  ++
Sbjct: 1   MQTTQQNA-PLKRTMKTRHLIMLSLGGVIGTGLFFNTGYIISTTGAAGTLLAYLIGALVV 59

Query: 61  FLTMLCLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQ 120
           +L M CLGEL+VA P +G+F  YA +++ PA G+   WLYWL W V     F +AG  MQ
Sbjct: 60  WLVMQCLGELSVAMPETGAFHVYAARYLGPATGYTVAWLYWLTWTVALGSSFTAAGFCMQ 119

Query: 121 RWFPHIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLI 180
            WFP + VW+WC+VF A++F LN I+T+ FAE EFWFS +K++ I+ FIILGGAA+FG I
Sbjct: 120 YWFPQVPVWVWCVVFCAIIFGLNVISTRFFAEGEFWFSLVKVVTIIAFIILGGAAIFGFI 179

Query: 181 DLKGGEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPR 240
            ++ G  AP L++   +G FP+G   +L+TM+ VNFAF GTELIG+AAGE+E+P K IP 
Sbjct: 180 PMQDGSPAPGLSNITAEGWFPHGGLPILMTMVAVNFAFSGTELIGIAAGETENPRKVIPV 239

Query: 241 SIKQTVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIAL 300
           +I+ T+ R ++FF+ ++ V+A +IP +Q GV +SPFV VFE++GIPYAADI NFVIL A+
Sbjct: 240 AIRTTIARLIIFFIGTVFVLAALIPMQQVGVEKSPFVLVFEKVGIPYAADIFNFVILTAI 299

Query: 301 LSVANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAE 360
           LS ANSGLYAS R+L++++NE        +  + GVP+ +L V+M    L+L +     +
Sbjct: 300 LSAANSGLYASGRMLWSLSNERTLPACFARVTKNGVPLTALSVSMLGGVLALFSSVVAPD 359

Query: 361 TVYMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLN 420
           TV++ L +++G +    W++I  S  +FRR+++++G  + +L ++ P YP++P++G  L 
Sbjct: 360 TVFVALSAISGFAVVAVWLSICASHFVFRRRHLQQGKALSELHYRAPWYPLVPVLGFVLC 419

Query: 421 TVVLISLAFDPEQRIALYCGVPFMIICYIIY 451
            V  + LAFDP QRIAL+CG+PF+ +CY  Y
Sbjct: 420 LVACVGLAFDPAQRIALWCGLPFVALCYGAY 450


Lambda     K      H
   0.329    0.142    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: 645
Number of extensions: 27
Number of successful extensions: 1
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: 467
Length of database: 467
Length adjustment: 33
Effective length of query: 434
Effective length of database: 434
Effective search space:   188356
Effective search space used:   188356
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