Align Amino-acid permease RocE (characterized)
to candidate H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__Burk376:H281DRAFT_04042 Length = 506 Score = 291 bits (745), Expect = 3e-83 Identities = 156/464 (33%), Positives = 260/464 (56%), Gaps = 12/464 (2%) Query: 1 MNTNQDNGNQ---LQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGG 57 + N DN Q L+R +K+RH+ +I+LGG IGTG FLG+ + AGP +L Y +GG Sbjct: 42 LGRNLDNALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGP-SMILGYAIGG 100 Query: 58 FIMFLTMLCLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQ 117 I F+ M LGE+ PV+GSF +A K+ GF GW YW+ + + E + G Sbjct: 101 VIAFMIMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGT 160 Query: 118 LMQRWFPHIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMF 177 + W+P + W+ LV A + +N KA+ E+EFWF+ IK++ ++ I+ GG + Sbjct: 161 YVHYWWPGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGG---Y 217 Query: 178 GLIDLKGGEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKT 237 L+ GG QA + G FP+G + + + F+F G ELIG+ A E+++P+K+ Sbjct: 218 LLVSGHGGPQASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKS 277 Query: 238 IPRSIKQTVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVIL 297 IP+++ Q ++R L+F++ S+ V+ + PW + SPFV +F QIG A+++N V+L Sbjct: 278 IPKAVNQVIYRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVL 337 Query: 298 IALLSVANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFA 357 A LSV NSG+YA++R+LY +A +G A +AL K ++RGVP ++ ++ ++ + Sbjct: 338 TAALSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYL 397 Query: 358 QAETVYMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGL 417 +L++L + + W ISL+ + RR + G E L FK+ +PV I L Sbjct: 398 IPAEALGLLMALVVAALVLNWALISLTHLKSRRAMVAAG---ETLVFKSFWFPVSNWICL 454 Query: 418 TLNTVVLISLAFDPEQRIALYCGVPFMIICYIIYHVVIKKRQQA 461 ++L+ LA P +++ ++++ + Y K+R+ A Sbjct: 455 AFMALILVILAMTPGLSVSVLLVPVWLVVMWAGY--AFKRRRAA 496 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: 573 Number of extensions: 25 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: 506 Length adjustment: 34 Effective length of query: 433 Effective length of database: 472 Effective search space: 204376 Effective search space used: 204376 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: 52 (24.6 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