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.
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:
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