Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate Ac3H11_3326 Amino acid ABC transporter, permease protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3326 Length = 260 Score = 82.4 bits (202), Expect = 1e-20 Identities = 64/206 (31%), Positives = 103/206 (50%), Gaps = 25/206 (12%) Query: 165 WPFVISVVLAIV-----AIVLMTRWANKRFEATGEPFHKFWVGLALFLVIPALSALLFGA 219 W +IS + +V A+ RWA R+ A+ WV P L +LF Sbjct: 61 WLTLISGSVGLVLGTGAALARTARWAVVRWAAS----FYIWV----IRGTPLLVQILF-- 110 Query: 220 PVHWEMPEL-KGFNFVGGWVLIPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAAR 278 V++ +P L G N +P+ A LAL + A+ AE +R+G+ +V GQTEAA+ Sbjct: 111 -VYFALPVLVPGLN-------LPDFAAAVLALGLNVGAYNAEAIRAGLLAVPRGQTEAAK 162 Query: 279 SLGLRNGPTLRKVIIPQALRVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQT 338 +LGL V+ PQA ++ +PPL S ++ L K+SSLA IG E+ ++ + + T Sbjct: 163 ALGLGRMHVFFDVVFPQAFKISLPPLVSNFVALLKDSSLAYAIGVVELTNV-GNRIQSAT 221 Query: 339 GQAIEVIAITMSVYLAISISISLLMN 364 Q I ++ YL ++ ++ + N Sbjct: 222 FQPIATLSTVAITYLLLTTLVTQISN 247 Score = 45.1 bits (105), Expect = 2e-09 Identities = 27/75 (36%), Positives = 42/75 (56%) Query: 61 SYARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLL 120 S A+ F G TL +T I + +LG +AR ++ ++ A+ Y+ V R P L+ Sbjct: 47 SNAQAFSDGARTTLWLTLISGSVGLVLGTGAALARTARWAVVRWAASFYIWVIRGTPLLV 106 Query: 121 QILFWYFAVFLSMPG 135 QILF YFA+ + +PG Sbjct: 107 QILFVYFALPVLVPG 121 Lambda K H 0.328 0.141 0.430 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: 189 Number of extensions: 7 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: 375 Length of database: 260 Length adjustment: 27 Effective length of query: 348 Effective length of database: 233 Effective search space: 81084 Effective search space used: 81084 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