Align Amino-acid permease RocE (characterized)
to candidate RR42_RS05070 RR42_RS05070 amino acid permease
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__Cup4G11:RR42_RS05070 Length = 466 Score = 293 bits (751), Expect = 6e-84 Identities = 151/450 (33%), Positives = 252/450 (56%), Gaps = 5/450 (1%) Query: 11 LQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGEL 70 L R++K L MI++GG IGTG F+G+GF I AGP G +LSY +G + L M CL E+ Sbjct: 8 LHRSLKPAQLAMIAIGGAIGTGLFMGSGFAIGFAGP-GVLLSYAIGALVTLLLMGCLAEM 66 Query: 71 AVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDVWI 130 VA P SGSF YA ++SP GF + YW + E + M WFP + W Sbjct: 67 TVAHPTSGSFGAYAEHYVSPLAGFLVRYAYWASIVLAVGTEVTAVALYMGYWFPQVPAWF 126 Query: 131 WCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQAPF 190 W + F+A + ++N + F E+ FS +KI+ I+ FI++ +FG G A Sbjct: 127 WIVSFSAALILINLVGVGIFGAVEYLFSMVKIVAIVAFILVAAYIVFGAPGSTGSGAAGA 186 Query: 191 LTHFY--EDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWR 248 H Y G PNG+ M + +I F++ E+I VAAGE++DPE+ + ++ + T+ R Sbjct: 187 GFHHYTAHGGFLPNGLWGMWVAVIVSIFSYLSIEMIAVAAGEAQDPERAVLQAFRSTMIR 246 Query: 249 TLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSGL 308 +F++L++ ++ ++PW QAG +SPFV V E I +P AA I+NFV+LIA LS NS L Sbjct: 247 LGLFYLLTLALMLAIVPWNQAGAQKSPFVQVMEAIHVPGAAAIINFVVLIAALSAMNSQL 306 Query: 309 YASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYMVLLS 368 Y +TR ++++A GQA ++ G+ ++RG+P+ +L+++ L+ ++++++ Sbjct: 307 YITTRTMFSLARAGQAPRSFGEVSKRGIPVRALLLSSIGIALATGLNVFYPGNAFLLMMA 366 Query: 369 LAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVLISLA 428 ++ A W I ++ FRR++ G + L F+ +P+L L+G + ++++ Sbjct: 367 ISMFGALFTWFMIFVTHYRFRRQWAAAGNR--PLAFRMRGFPLLTLLGAGMMLAIMLTTL 424 Query: 429 FDPEQRIALYCGVPFMIICYIIYHVVIKKR 458 R+ L G+PF+ + Y + + R Sbjct: 425 LTDAFRMTLITGIPFLAALSVAYLLRFRHR 454 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: 484 Number of extensions: 20 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: 466 Length adjustment: 33 Effective length of query: 434 Effective length of database: 433 Effective search space: 187922 Effective search space used: 187922 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