Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate SMc03133 SMc03133 amino-acid transport system permease ABC transporter protein
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__Smeli:SMc03133 Length = 323 Score = 90.5 bits (223), Expect = 7e-23 Identities = 60/158 (37%), Positives = 92/158 (58%), Gaps = 11/158 (6%) Query: 259 LFAPISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQ 318 LF + L+ +L PQ+ G+ ++ + A ++AL+L A++ EI RAGI+ Sbjct: 164 LFRGLPLLMQIYIIYLGLPQV-------GY-VISAVPAGILALSLCYGAYMTEIFRAGIE 215 Query: 319 AISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLR 378 +I RGQTE A ALGL P +TM LVILPQA+RVI+PP +QF+ + K+SSL V +L Sbjct: 216 SIPRGQTEGATALGLSPSQTMGLVILPQAMRVIIPPTGNQFIAMLKDSSLISVVGVWELM 275 Query: 379 GTLGGITLNQTG-RELECMLLMMLIYLTISLTISSLMN 415 T QT R +E ++ +IY +S+ + + + Sbjct: 276 YL--ARTQGQTEFRHIEMLITASMIYWILSIGLEYMQS 311 Score = 44.7 bits (104), Expect = 4e-09 Identities = 18/58 (31%), Positives = 37/58 (63%) Query: 90 EGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIPLLLWILLM 147 +G++ TL +SV+ +AT++ + + +LS+N ++ + T Y FR +PLL+ I ++ Sbjct: 120 QGVVTTLYISVISIAVATVIALVGAIAKLSKNGVIYGLATFYTSLFRGLPLLMQIYII 177 Lambda K H 0.326 0.139 0.419 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: 294 Number of extensions: 14 Number of successful extensions: 2 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: 426 Length of database: 323 Length adjustment: 30 Effective length of query: 396 Effective length of database: 293 Effective search space: 116028 Effective search space used: 116028 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: 49 (23.5 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