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 BPHYT_RS15605 BPHYT_RS15605 ABC transporter permease
Query= TCDB::Q8YXD0 (288 letters) >FitnessBrowser__BFirm:BPHYT_RS15605 Length = 316 Score = 134 bits (338), Expect = 2e-36 Identities = 93/315 (29%), Positives = 167/315 (53%), Gaps = 40/315 (12%) Query: 1 MDIQTIQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNTFGV- 59 MDI IQ ++NG+ +GS+ A+ A+G T+ YGIL + NFAHGD L +GA + ++ GV Sbjct: 1 MDI-FIQQVLNGLVLGSVYAIIALGYTMVYGILGIINFAHGDVLMVGAMVA--LSAIGVL 57 Query: 60 -----------NIWLSMIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFL 108 + +++I+A + V E++ + +R +A +I +IG+++ L Sbjct: 58 QNHFPGLGNVPTLIIALIIAAIVCAAVGYTIERVAYRPLR--KAPRLAPLITAIGVSILL 115 Query: 109 RNGIILIWGGRNQNY-NLPITPALDIF-------GVKVPQNQLLVLALAVLSIGALHYLL 160 + ++IW + L T L++ G + +++++ +A L +G L L+ Sbjct: 116 QTLAMMIWSRNPLPFPQLLPTDPLNVIKATDTTPGAVISMTEIVIIVVAFLVMGGLLLLV 175 Query: 161 QNTKIGKAMRAVADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSM----YGLITAVRP 216 TK+G+AMRA+A++ A + G++ VI T++I + +L G M YG Sbjct: 176 HKTKLGRAMRAIAENPGNASLMGVNPNFVISATFMIGSALAALAGVMIASEYG---NAHF 232 Query: 217 NMGWFLILPLFASVILGGIGNPYGAIAAAFIIGIVQEVSTPFL--------GSQYKQGVA 268 MG+ L F + +LGGIGN GA+ I+G+++++ ++ GS Y+ A Sbjct: 233 YMGFIPGLKAFTAAVLGGIGNLGGAMVGGVILGLIEQLGAGYIGNLTGGVFGSNYQDVFA 292 Query: 269 LLIMILVLLIRPKGL 283 +++I+VL+ RP GL Sbjct: 293 FIVLIIVLVFRPSGL 307 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: 273 Number of extensions: 19 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: 288 Length of database: 316 Length adjustment: 27 Effective length of query: 261 Effective length of database: 289 Effective search space: 75429 Effective search space used: 75429 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