Align Amino-acid permease RocE (characterized)
to candidate WP_057509355.1 ABB28_RS14795 amino acid permease
Query= SwissProt::P39137 (467 letters) >NCBI__GCF_001431535.1:WP_057509355.1 Length = 460 Score = 253 bits (645), Expect = 1e-71 Identities = 144/427 (33%), Positives = 234/427 (54%), Gaps = 9/427 (2%) Query: 10 QLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGE 69 +L +K R L M+ LG IG G FLG+G + AGP +LSYLV G ++ + M LGE Sbjct: 15 RLGHALKPRQLIMMGLGSAIGAGLFLGSGVGVQLAGP-AVLLSYLVAGALVIIVMNALGE 73 Query: 70 LAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDVW 129 +A P SG+F YA + P G GWL+W+ + A E + A L+ + + V Sbjct: 74 MAANKPTSGAFSVYAADALGPTAGATVGWLWWVQLVIVIAAEAVGAAGLLATVWTGLSVP 133 Query: 130 IWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQAP 189 + L F +N + K F E EFWF+ +K+ IL FI +G A + G + +P Sbjct: 134 MAALAFMLFFTAINLLGVKNFGEFEFWFAILKVAAILGFIAIGAALLLGWLP---DATSP 190 Query: 190 FLTHFYEDGLF-PNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWR 248 L++F +G F P G+ + ++ V FAF GTE++ VAA E+EDPE++I R+I+ WR Sbjct: 191 GLSNFTGNGGFAPTGLAGVGAALLVVIFAFGGTEIVAVAAAETEDPERSIARAIRTVAWR 250 Query: 249 TLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSGL 308 LVF++ S+ VI ++PW + ++SPF AV E IP A + V +IALLS N+ L Sbjct: 251 ILVFYIGSLSVIIAVVPW-TSEALKSPFAAVLEAANIPGAGTAITLVAVIALLSALNANL 309 Query: 309 YASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYMVLLS 368 Y ++R+++++A +A LG ++R VP+ +++ ++ + + + + V VLL+ Sbjct: 310 YGASRMIFSLAQRREAPAVLGWADRRQVPVLAVLASVLFGFAATVMELVFPDRVLPVLLN 369 Query: 369 LAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVLISLA 428 + G + + W LSQ++ RR+ R G L F+ +P L + L + ++ L Sbjct: 370 IVGSTCLLVWTLSLLSQLVLRRRADRAG---VALPFRMAAFPWLTALALAILALIFALLL 426 Query: 429 FDPEQRI 435 + + R+ Sbjct: 427 YGDQTRL 433 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: 507 Number of extensions: 21 Number of successful extensions: 3 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: 460 Length adjustment: 33 Effective length of query: 434 Effective length of database: 427 Effective search space: 185318 Effective search space used: 185318 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 24 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