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 PfGW456L13_4608 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= TCDB::Q8YXD0 (288 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4608 Length = 307 Score = 139 bits (350), Expect = 8e-38 Identities = 81/294 (27%), Positives = 159/294 (54%), Gaps = 21/294 (7%) Query: 7 QLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFF---------VNTF 57 Q +VNG+ +GS AL A+G T+ YGI+ + NFAHG+ +G+Y+ F +++ Sbjct: 9 QQLVNGLTIGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMLGLDSV 68 Query: 58 GVNIWLSMIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWG 117 + + + + +V T E++ + +R +N +I +IG+++FL+N ++L Sbjct: 69 PLLMTAAFLATIVVTSAYGYSIERIAYRPLRG--SNRLIPLISAIGMSIFLQNTVLLAQD 126 Query: 118 GRNQNYNLP-ITPALDIFG------VKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMR 170 ++++ +P + P FG V + Q++V + ++++ L + +++G+A R Sbjct: 127 SKDKS--IPNLIPGNFAFGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRACR 184 Query: 171 AVADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGL-ITAVRPNMGWFLILPLFAS 229 A A+D+ +A + GI+ +I T++I + ++ + + + PN G+ + L F + Sbjct: 185 ACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFTA 244 Query: 230 VILGGIGNPYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGL 283 +LGGIG+ GA+ ++G+ + G QYK VA +++LVLL RP GL Sbjct: 245 AVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGL 298 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: 242 Number of extensions: 17 Number of successful extensions: 5 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: 307 Length adjustment: 26 Effective length of query: 262 Effective length of database: 281 Effective search space: 73622 Effective search space used: 73622 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