Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Dsui_0629 Dsui_0629 branched-chain amino acid ABC-type transport system, permease component
Query= TCDB::P74318 (286 letters) >FitnessBrowser__PS:Dsui_0629 Length = 307 Score = 146 bits (369), Expect = 5e-40 Identities = 96/302 (31%), Positives = 170/302 (56%), Gaps = 34/302 (11%) Query: 5 QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTSGINLWLSMA 64 Q I NG+ +GSI AL A+G T+ YGIL L NFAHG+ + + A T+ + L Sbjct: 6 QQIINGLVLGSIYALVALGYTMVYGILGLINFAHGEVVMIGAL------TALTVVKLLAG 59 Query: 65 LGCVGTIIA-----------MFIG---EWLLWKPMRARRATATTLIIISIGLALFLRNGI 110 G G +IA M IG E + ++P+R +A +I +IG+++ L+N Sbjct: 60 SGLPGPVIALIGLMAAAPVCMAIGYGIEKIAYRPLR--KAPRLAPLITAIGVSIVLQNLA 117 Query: 111 LLIWGGNNQNYRVPIVPAQ--DFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMR 168 +++WG + ++ ++PA+ + +G F +++++ +A M L L++ RT++G+AMR Sbjct: 118 MMVWGRSYHSFPA-VLPAEAHEVLGATFTDLQVIIVLVAAGMMAGLLLLINRTRLGRAMR 176 Query: 169 AVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKP-NMGWFLILPMFAS 227 A A+N +A++ G+NV ++ T+V+ + L A+ G M ++ MG+ L L F + Sbjct: 177 ATAENPAIAQLMGVNVNHIISLTFVIGSALAAVAGLMVSANYSIAHYYMGFILGLKAFTA 236 Query: 228 VILGGIGNPYGAIAGGIIIGVAQ--------EVSVPWFGTSYKMGVALLLMIIILFIRPQ 279 +LGGIGN GA+ GGI++G+ + +++ + G+ Y+ A ++I++L RP Sbjct: 237 AVLGGIGNLAGAMIGGILLGLIESLGAGYIGDITGGFLGSHYQDVFAFFVLILVLVFRPS 296 Query: 280 GL 281 GL Sbjct: 297 GL 298 Lambda K H 0.329 0.143 0.450 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: 195 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: 286 Length of database: 307 Length adjustment: 26 Effective length of query: 260 Effective length of database: 281 Effective search space: 73060 Effective search space used: 73060 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 (21.8 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