Align NatC aka SLL0146, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 8501894 DvMF_2609 inner-membrane translocator (RefSeq)
Query= TCDB::P74455 (372 letters) >FitnessBrowser__Miya:8501894 Length = 415 Score = 89.7 bits (221), Expect = 1e-22 Identities = 69/212 (32%), Positives = 104/212 (49%), Gaps = 9/212 (4%) Query: 5 YLIFLITSAATYGIFALGLNLQWGFAGLINFGHVAFMTLGAYATTLLSLR-GLPIPLAVL 63 Y ++ SA Y + LGLN+ G +G + G+VAF +GAY+ +L+ GL + Sbjct: 111 YQTNIMISALLYVMLGLGLNIVVGLSGQLVLGYVAFYAVGAYSYAILNSNFGLGFWSVLP 170 Query: 64 VGMGLAMALGLLIGTSTLRLREDYLAIVTIGVSELIRLIANNEEWLTQGTFGVQSFPWPM 123 +G +A G+L+G LRLR DYLAIVT+G E+IRL+ N +QG G+ + P Sbjct: 171 IGGAMAALFGILLGFPVLRLRGDYLAIVTLGFGEIIRLVLENWSSFSQGPSGIANIERPG 230 Query: 124 DFNPTL-LSRIVFVIWLTVLTIYAESILIKSLLKQWKEGKKIQGKSYQPRKPLALLIWGI 182 L +S I+ +L +IL + LK + G+ Q +A GI Sbjct: 231 LLGMQLSVSDATTYIYYLILAAVIVTILAVTRLKNSRIGRAWQALR---EDEIACQAMGI 287 Query: 183 ITTALILTAYVPGVVSLYNYSGKAGLMLLALT 214 T LTA+ G ++G AG++ A T Sbjct: 288 DITTTKLTAFALGAC----WAGFAGVIFAAKT 315 Score = 72.4 bits (176), Expect = 2e-17 Identities = 51/154 (33%), Positives = 82/154 (53%), Gaps = 16/154 (10%) Query: 211 LALTLLALTYAGLEFWVHSPWGRILKAIREDEEIPRALGKNVFWYKLQAFMGGGAIAGLA 270 L L + +T + +S GR +A+REDE +A+G ++ KL AF G AG A Sbjct: 248 LILAAVIVTILAVTRLKNSRIGRAWQALREDEIACQAMGIDITTTKLTAFALGACWAGFA 307 Query: 271 GALFAWQLTSIYPSNFDTLLTFNAWIIVVLGGAGSNAGTVLGTIIFWAYDSLTRFLLPQI 330 G +FA + T I P++F L + +VVLGG GS G +G ++ LLP+ Sbjct: 308 GVIFAAKTTFINPASFTFLESAMVLAMVVLGGMGSVIGVSVGALVL--------ILLPEY 359 Query: 331 --AFLDQSQAGALRVMVIGLILMVLMVWRPQGIL 362 AF + R+++ G ++++MV+RPQG++ Sbjct: 360 LRAFSE------YRMLIFGATMVLMMVFRPQGLV 387 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: 398 Number of extensions: 23 Number of successful extensions: 4 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: 415 Length adjustment: 31 Effective length of query: 341 Effective length of database: 384 Effective search space: 130944 Effective search space used: 130944 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