Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate HSERO_RS22215 HSERO_RS22215 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__HerbieS:HSERO_RS22215 Length = 323 Score = 191 bits (485), Expect = 2e-53 Identities = 106/303 (34%), Positives = 182/303 (60%), Gaps = 4/303 (1%) Query: 27 LPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGSILA 86 L L+ ++L +++ + F++ ++ ++L ++I +LA+ VILT+GIDLSV S LA Sbjct: 2 LALLTVVLILLVGVRAPVFLSAQSMDNLLTDSAITIMLALAQMLVILTRGIDLSVASNLA 61 Query: 87 FAGLCSAMVATQGYGLLAAVSAGM--FAGAMLGVVNGFMVANLSIPPFVATLGMLSIARG 144 +G+ SA++A L V M G MLG++NG+++ L +PP V TLG +S+ RG Sbjct: 62 LSGMMSALLAMHFPALPVGVFILMAVLIGLMLGLLNGWLIGYLELPPIVVTLGSMSVYRG 121 Query: 145 MTFILNDGSPIT--DLPDAYLALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYGRYVYA 202 M F+L+ G+ ++ ++P ++A + ++G + + + A+ + W + R+T +GR +YA Sbjct: 122 MVFVLSGGAWVSSRNMPADFIAFPLARLGGLTHLVWLGALAVVAIWFLARHTRFGRDLYA 181 Query: 203 VGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAV 262 +G + +A GI R + Y +SG +AGLAG + AR A + +EL IAA Sbjct: 182 IGNDPAAAAYVGIASRGRLLWTYGLSGAMAGLAGYLWVARYAVAYTEIAYGFELTVIAAC 241 Query: 263 VIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRK 322 VIGG S++GG G + G + GAL + VINN L ++ +S ++Q GL+I+ AV+++ K Sbjct: 242 VIGGVSIAGGVGQVSGAVLGALFLSVINNALPIMRISPFWQSALTGLVILCAVVLNARGK 301 Query: 323 KKR 325 + R Sbjct: 302 QGR 304 Lambda K H 0.326 0.141 0.412 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: 243 Number of extensions: 16 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: 325 Length of database: 323 Length adjustment: 28 Effective length of query: 297 Effective length of database: 295 Effective search space: 87615 Effective search space used: 87615 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 (21.6 bits) S2: 48 (23.1 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