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 AZOBR_RS21005 AZOBR_RS21005 branched-chain amino acid ABC transporter
Query= TCDB::Q8YXD0 (288 letters) >FitnessBrowser__azobra:AZOBR_RS21005 Length = 294 Score = 164 bits (414), Expect = 3e-45 Identities = 96/282 (34%), Positives = 165/282 (58%), Gaps = 6/282 (2%) Query: 6 IQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNTF-GVNIWLS 64 +QL+V+G+ +G I AL ++GLTL +G+ R+ NFAHGDF+ +G YLT+ +N++ G++ +L Sbjct: 6 VQLVVSGLLLGGIYALISIGLTLIFGVSRIKNFAHGDFVMVGMYLTYVLNSWSGLDSYLV 65 Query: 65 MIVAVVGTVGVMLLSEKLLWSRMRSIR-ANSTTLIIISIGLALFLRNGIILIWGGR-NQN 122 +++ T + L L W+ +R I+ A I ++GL L L+N ++I+GG Sbjct: 66 LLIV---TPLMFLFGLFLSWAIIRPIQGAPQVAQIFATVGLGLVLQNVTLMIFGGDFRTT 122 Query: 123 YNLPITPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDLAKVS 182 ++ L I + +P L+ A+A+ + ++ L+ + GKAMRAVA D A + Sbjct: 123 ASVFAGKVLRIGDIALPAPLLIAFAVAMAVVAVIYLFLKTSYTGKAMRAVAQDRRSASLM 182 Query: 183 GIDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGNPYGAI 242 IDV+ + +T+ + L G++ + V P +G L+L F V+LGG+G+ GA+ Sbjct: 183 SIDVKGIDLFTFGLGTACAGLTGALLAPMFPVYPTVGINLVLIAFVVVVLGGLGSIAGAL 242 Query: 243 AAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGLF 284 IG+++ +S F+GS+ +Q L+ + VLL+RP GLF Sbjct: 243 IGGLAIGLIETLSGFFIGSEMRQMAYFLVFLAVLLLRPAGLF 284 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: 246 Number of extensions: 15 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: 294 Length adjustment: 26 Effective length of query: 262 Effective length of database: 268 Effective search space: 70216 Effective search space used: 70216 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