Align Amino-acid permease RocE (characterized)
to candidate AO353_24825 AO353_24825 amino acid transporter
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24825 Length = 470 Score = 537 bits (1383), Expect = e-157 Identities = 246/452 (54%), Positives = 344/452 (76%) Query: 8 GNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCL 67 G L R +KSRH+FM+SLGGVIGTG F+G+G TINQ GP+GA+L+YL+ GF+M+L M+CL Sbjct: 9 GIHLTRALKSRHIFMLSLGGVIGTGLFMGSGVTINQGGPVGAILAYLIAGFLMYLVMVCL 68 Query: 68 GELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHID 127 GEL+V PVSGSFQT+ATKFI PA GF GW+YW+ WA T +EF +AG LM RWFP + Sbjct: 69 GELSVQMPVSGSFQTHATKFIGPATGFMIGWVYWMSWASTVGLEFTAAGMLMVRWFPTVP 128 Query: 128 VWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQ 187 +W W +F ++F LNA+ T+AF E+E+WFSGIK+ IL FI++G +FG I L G Sbjct: 129 IWYWSALFVVVLFGLNALATRAFGEAEYWFSGIKVAAILGFIVVGVLVIFGAIPLTSGAP 188 Query: 188 APFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVW 247 AP +++ D LFPNG+ A+ M+TV +AFQG E++GVAAGE++ PEK+IPR+++ V+ Sbjct: 189 APMMSNLIGDSLFPNGLPAVFAVMMTVVYAFQGCEIMGVAAGETDQPEKSIPRAVRNVVF 248 Query: 248 RTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSG 307 R L+F+VL+I+V++ ++PW+QAG++ESPFV VF+ +GIPYAAD+MNFVIL A+LSV NSG Sbjct: 249 RVLIFYVLAIVVLSAIVPWQQAGLMESPFVQVFDMVGIPYAADLMNFVILTAILSVGNSG 308 Query: 308 LYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYMVLL 367 LYASTRIL+AM+ G A K+L ++RGVP+ +L +T+ A +SL+T F A+T++MVL+ Sbjct: 309 LYASTRILWAMSKTGMAPKSLSPLSKRGVPLRALSITLCFALVSLMTSFIAADTLFMVLM 368 Query: 368 SLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVLISL 427 +++GMS V WI I+L+Q FRR YIR+GGK+ DLK++ P +P+LP++ + L + + L Sbjct: 369 AVSGMSGTVTWIVIALAQYKFRRAYIRDGGKLSDLKYRAPWFPLLPILCIALCCSLFVFL 428 Query: 428 AFDPEQRIALYCGVPFMIICYIIYHVVIKKRQ 459 A D QR +LY G FM +CY Y ++ +KRQ Sbjct: 429 AMDETQRPSLYWGFGFMALCYGAYFLIQRKRQ 460 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: 28 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: 470 Length adjustment: 33 Effective length of query: 434 Effective length of database: 437 Effective search space: 189658 Effective search space used: 189658 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