Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate GFF1059 Psest_1092 Branched-chain amino acid ABC-type transport system, permease components
Query= TCDB::Q8YXD0 (288 letters) >FitnessBrowser__psRCH2:GFF1059 Length = 295 Score = 128 bits (322), Expect = 1e-34 Identities = 82/278 (29%), Positives = 155/278 (55%), Gaps = 10/278 (3%) Query: 12 GIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFF-VNTFGVNIWLSMIVA-- 68 G+ G+ AL ++GL + +G+LR+ NFAHG LGA++ F +N GV+ W ++++A Sbjct: 19 GLINGAFYALLSLGLAIIFGLLRIINFAHGAQYMLGAFVAFLGLNYLGVSYWFALVLAPL 78 Query: 69 VVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGGRNQNYNLP-- 126 VVG +G+ + E+ L R+ + ++++ GLAL + + ++G +Y +P Sbjct: 79 VVGCLGMAI--ERGLLRRIAG--EDHLYGLLLTFGLALIVEGSFVKLFGVSGSSYPMPEL 134 Query: 127 ITPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDLAKVSGIDV 186 + ++ + +P + V+ A++ A Y+++ T++G +RA ++ L + GI+V Sbjct: 135 LRGGFNLGFMFLPTYRAWVIVAALVVCLATWYVIERTRLGSYLRAGTENPKLMQGFGINV 194 Query: 187 EQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGNPYGAIAAAF 246 ++ T+ + + G + I AV P MG L++ +FA V++GG+G+ GAI Sbjct: 195 PLLVTLTYGYGVALAAFAGVLAAPIYAVTPGMGSNLLIVVFAVVVIGGMGSILGAIVTGI 254 Query: 247 IIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGLF 284 +G+++ ++ F + V L+M+ VLLIRP GLF Sbjct: 255 AMGLIEGLTKVFY-PEAANTVVFLVMVAVLLIRPAGLF 291 Lambda K H 0.328 0.144 0.426 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: 270 Number of extensions: 14 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: 288 Length of database: 295 Length adjustment: 26 Effective length of query: 262 Effective length of database: 269 Effective search space: 70478 Effective search space used: 70478 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 (21.7 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