GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Keio:14398 b0260 putative amino acid/amine
           transport protein (VIMSS)
          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 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