Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate H281DRAFT_05513 H281DRAFT_05513 branched-chain amino acid transport system permease protein
Query= TCDB::Q8DQH8 (254 letters) >FitnessBrowser__Burk376:H281DRAFT_05513 Length = 597 Score = 184 bits (468), Expect = 3e-51 Identities = 104/250 (41%), Positives = 157/250 (62%), Gaps = 7/250 (2%) Query: 4 LEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTLD 63 L V+ ++K +GG+ AV DV+ + G++ GLIGPNGAGK+TL NL+ G Y G V LD Sbjct: 346 LTVESVSKQYGGVLAVSDVSFSVAAGQIHGLIGPNGAGKSTLVNLIAGNYLCDSGRVRLD 405 Query: 64 GHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHV--FTSFLRLPAF 121 G ++ A GL RTFQN++L + L VL+NVL+ + HV F + AF Sbjct: 406 GADVSNLVTADRAKRGLARTFQNLQLVEALPVLENVLLGMSS-ADGHVANFAKWWMGRAF 464 Query: 122 YKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAG 181 E+ +ALE+L F ++ + LSYG ++ +E+ RA+A P+++ LDEP AG Sbjct: 465 DLPERR---EALEILAFFGIEHLCQAYPTELSYGHRKLVELARAIAQRPRLMLLDEPIAG 521 Query: 182 MNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKT 241 +N E E+ +++ R++D +TI+LIEH+M VM + + I VLE GRLI GTP+EI++ Sbjct: 522 LNGAEAMEVAKVVGRLRDA-GVTILLIEHNMEFVMSLCDSISVLEQGRLIGTGTPEEIRS 580 Query: 242 NKRVIEAYLG 251 ++R++ AYLG Sbjct: 581 DERILRAYLG 590 Lambda K H 0.319 0.139 0.385 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: 316 Number of extensions: 9 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: 254 Length of database: 597 Length adjustment: 30 Effective length of query: 224 Effective length of database: 567 Effective search space: 127008 Effective search space used: 127008 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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