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 3608585 Dshi_1979 inner-membrane translocator (RefSeq)
Query= TCDB::Q8YXD0 (288 letters) >FitnessBrowser__Dino:3608585 Length = 305 Score = 170 bits (430), Expect = 4e-47 Identities = 104/301 (34%), Positives = 174/301 (57%), Gaps = 25/301 (8%) Query: 6 IQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNTFGVNIWLSM 65 IQ +++GI VG+I++L A+GLTLT +LR +NF+H + L++GAY + + ++ Sbjct: 2 IQHLLDGILVGAILSLGAIGLTLTMHMLRFANFSHAELLSIGAYAALVFDALFSALLPAL 61 Query: 66 IVAV----------VGTVGVMLLS-------EKLLWSRMRSIRANSTTLIIISIGLALFL 108 A+ + TV M L+ ++L++ R+R + +++ S G+A+ + Sbjct: 62 QTAIPPLSLTWTLSLATVASMALTGLSAIAIDRLIFKRVRE-KGGELSMVFASFGVAMVI 120 Query: 109 RNGIILIWGGRNQNYNLPITPAL-----DIFGVKVPQNQLLVLALAVLSIGALHYLLQNT 163 RN I L +G Q Y+ I A + VK Q LV ALA++ + LH +L T Sbjct: 121 RNLIGLGFGLNTQLYSDDIVFATVLSRDPLILVKPDQVFTLVAALAIMVV--LHLVLSRT 178 Query: 164 KIGKAMRAVADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLI 223 G ++RAVA++ LA+VSGI++++++ W++ GT+ + G YGL + P +G L+ Sbjct: 179 TFGYSLRAVAENPVLAQVSGINLQRMVALIWILGGTLAAAAGVFYGLTNQITPVIGRDLV 238 Query: 224 LPLFASVILGGIGNPYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGL 283 LP+FA+ I+GGIG+ YGA+ F++GI ++ L S Y V LI++ VL++RP GL Sbjct: 239 LPIFAATIVGGIGSIYGAVLGGFLVGIAANLALVVLPSGYSPSVPFLILVAVLVLRPHGL 298 Query: 284 F 284 F Sbjct: 299 F 299 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: 253 Number of extensions: 11 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: 305 Length adjustment: 26 Effective length of query: 262 Effective length of database: 279 Effective search space: 73098 Effective search space used: 73098 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