Align NatC aka SLL0146, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 209488 DVU0549 high-affinity branched-chain amino acid ABC transporter, permease protein
Query= TCDB::P74455 (372 letters) >MicrobesOnline__882:209488 Length = 407 Score = 91.3 bits (225), Expect = 4e-23 Identities = 70/212 (33%), Positives = 103/212 (48%), Gaps = 9/212 (4%) Query: 5 YLIFLITSAATYGIFALGLNLQWGFAGLINFGHVAFMTLGAYATTLLSLR-GLPIPLAVL 63 Y ++ SA Y + LGLN+ G +G + G+VAF +GAYA LL+ GL + Sbjct: 110 YQTNIMISALLYVMLGLGLNIVVGLSGQLVLGYVAFYAVGAYAYALLNADFGLGFWTVLP 169 Query: 64 VGMGLAMALGLLIGTSTLRLREDYLAIVTIGVSELIRLIANNEEWLTQGTFGVQSFPWPM 123 +G LA G+L+G LRL+ DYLAIVT+G E++RL+ N +T+G G+ P Sbjct: 170 IGGALAAVFGILLGFPVLRLKGDYLAIVTLGFGEIVRLVLENWGSVTRGPSGISKIARPG 229 Query: 124 DFNPTL-LSRIVFVIWLTVLTIYAESILIKSLLKQWKEGKKIQGKSYQPRKPLALLIWGI 182 F L +S I+ +L +I LK + G+ Q +A GI Sbjct: 230 LFGMELSVSEATTYIYYLILAAVIFTIFAVGRLKDSRIGRAWQALR---EDEIACEAMGI 286 Query: 183 ITTALILTAYVPGVVSLYNYSGKAGLMLLALT 214 T LTA+ G ++G AG++ A T Sbjct: 287 DLTTTKLTAFALGAC----WAGFAGVIFAAKT 314 Score = 74.3 bits (181), Expect = 5e-18 Identities = 49/133 (36%), Positives = 74/133 (55%), Gaps = 16/133 (12%) Query: 232 GRILKAIREDEEIPRALGKNVFWYKLQAFMGGGAIAGLAGALFAWQLTSIYPSNFDTLLT 291 GR +A+REDE A+G ++ KL AF G AG AG +FA + T I P++F L + Sbjct: 268 GRAWQALREDEIACEAMGIDLTTTKLTAFALGACWAGFAGVIFAAKTTFINPASFTFLES 327 Query: 292 FNAWIIVVLGGAGSNAGTVLGTIIFWAYDSLTRFLLPQI--AFLDQSQAGALRVMVIGLI 349 +VVLGG GS G VLG ++ LLP+ AF + R+++ G Sbjct: 328 AMILAMVVLGGMGSTLGVVLGALVL--------ILLPEYLRAFSE------YRMLIFGAA 373 Query: 350 LMVLMVWRPQGIL 362 ++++MV+RPQG++ Sbjct: 374 MVLMMVFRPQGLV 386 Lambda K H 0.327 0.143 0.442 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: 395 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 372 Length of database: 407 Length adjustment: 30 Effective length of query: 342 Effective length of database: 377 Effective search space: 128934 Effective search space used: 128934 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: 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