Align Amino-acid permease RocE (characterized)
to candidate Pf6N2E2_4959 S-methylmethionine permease
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4959 Length = 476 Score = 476 bits (1224), Expect = e-139 Identities = 219/449 (48%), Positives = 325/449 (72%), Gaps = 1/449 (0%) Query: 12 QRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGELA 71 ++ M++RH+ M++LGGVIGTG FL +G+T+NQAGP+GAV++Y++G ++++ M+CLGELA Sbjct: 15 KQEMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPMGAVIAYIIGALMVYMVMMCLGELA 74 Query: 72 VAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDVWIW 131 V P +GSF TYAT+F+ P G+ WLYWL W V EF +AG LM RWFP VWIW Sbjct: 75 VQMPETGSFSTYATRFLGPGTGYTVAWLYWLTWTVAIGSEFTAAGILMSRWFPDTPVWIW 134 Query: 132 CLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQAPFL 191 +FA ++F+ N I+ + FAE+EFW S IK+L +++F+++GG A+ GL+++ L Sbjct: 135 SALFAGVVFLSNVISVRLFAETEFWLSLIKVLTVVVFLLIGGGAILGLLNIDQAHSIG-L 193 Query: 192 THFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWRTLV 251 ++F +GLFP G + +T++ V+FAF GTELIG+AAGE++DP++ +PR+I+ TV R V Sbjct: 194 SNFTREGLFPTGFMPIAMTLLAVSFAFSGTELIGIAAGETKDPQRNVPRAIRTTVLRLAV 253 Query: 252 FFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSGLYAS 311 FFV +I V+A ++P +QAG+VESPFV VF IGIPY+ADIMNFVI+ ALLS ANSGLYA+ Sbjct: 254 FFVGTIFVLATLLPREQAGLVESPFVTVFTYIGIPYSADIMNFVIISALLSAANSGLYAA 313 Query: 312 TRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYMVLLSLAG 371 +R+L+ ++++G K + G P+ ++IV+MA SLL+ A+T+Y+ L+S++G Sbjct: 314 SRMLWTLSDQGHLPKQFSALTRMGTPLNAIIVSMAGGAASLLSSVFAADTIYLALVSISG 373 Query: 372 MSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVLISLAFDP 431 ++ V W++I+ SQI FRR Y+ GG I LKF+ YP +PL L ++ I +AFDP Sbjct: 374 LAVVVVWMSIAASQIAFRRHYVANGGDIRKLKFRVRGYPWVPLGALVCCSLACIGIAFDP 433 Query: 432 EQRIALYCGVPFMIICYIIYHVVIKKRQQ 460 EQR+ALY G+PF+ CY +Y++ K R++ Sbjct: 434 EQRVALYFGLPFIAWCYFVYYITRKSRER 462 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: 585 Number of extensions: 17 Number of successful extensions: 2 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: 476 Length adjustment: 33 Effective length of query: 434 Effective length of database: 443 Effective search space: 192262 Effective search space used: 192262 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