Align Amino-acid permease RocE (characterized)
to candidate GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__psRCH2:GFF1660 Length = 464 Score = 298 bits (762), Expect = 3e-85 Identities = 166/450 (36%), Positives = 258/450 (57%), Gaps = 19/450 (4%) Query: 11 LQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGEL 70 LQR +K+RH+ +I+LGG IGTG FLG+ + AGP +L Y +GGFI FL M LGE+ Sbjct: 11 LQRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGP-SMILGYAIGGFIAFLIMRQLGEM 69 Query: 71 AVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDVWI 130 V PV+GSF +A K+ GF GW YW+ + + E + G+ +Q W+P + W Sbjct: 70 IVEEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPTWA 129 Query: 131 WCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQAPF 190 F L+ ++N KAF E+EFWF+ +K+ I+ I+LG +F L+ KGGEQA Sbjct: 130 TAAAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLG---LFLLVSGKGGEQASI 186 Query: 191 LTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWRTL 250 + G FPNG ML+ + + F+F G EL+G+ A E+ +P+ IP++I Q V+R L Sbjct: 187 SNLWSHGGFFPNGFSGMLLALAIIMFSFGGLELVGITAAEAAEPKTVIPKAINQVVYRIL 246 Query: 251 VFFVLSIIVIAGMIPWK-------QAG--VVESPFVAVFEQIGIPYAADIMNFVILIALL 301 +F++ ++ V+ + PW AG SPFV +F IG AA ++NFV+L A L Sbjct: 247 IFYIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTAAHLLNFVVLTAAL 306 Query: 302 SVANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAET 361 SV NSG+Y ++R+LY +A +G A ++L K N RGVP+ ++ V+ V L + + + Sbjct: 307 SVYNSGVYCNSRMLYGLAEQGDAPRSLMKINSRGVPVLAVGVSALVTLLCVAVNYLFPQG 366 Query: 362 VYMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNT 421 +L+SLA + + W ISL+ + FRR ++G + FK +P+ + L Sbjct: 367 ALELLMSLAVAALVINWAMISLAHLKFRRAMQQQG---VEPSFKAFWFPLSNYLCLAFVA 423 Query: 422 VVLISLAFDPEQRIALYC---GVPFMIICY 448 +LI + + P R++++ V F+ +CY Sbjct: 424 GILIIMLWLPGIRMSVFAIPVWVGFLWLCY 453 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: 560 Number of extensions: 34 Number of successful extensions: 4 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: 464 Length adjustment: 33 Effective length of query: 434 Effective length of database: 431 Effective search space: 187054 Effective search space used: 187054 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