Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate HSERO_RS00315 HSERO_RS00315 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >FitnessBrowser__HerbieS:HSERO_RS00315 Length = 250 Score = 87.0 bits (214), Expect = 5e-22 Identities = 72/234 (30%), Positives = 116/234 (49%), Gaps = 29/234 (12%) Query: 159 LVAEGFWPFVISVVLAIVAIVLMTRWANKR-FEATGEPFHKFWVGLALFLV---IPALSA 214 L EG W +++ AI+ ++ T W E H FW + V I + Sbjct: 16 LFVEGTW---MTLKAAIICVIAGTCWGLVLGVGRLAEARHGFWKYFLCYCVQWPIRFYVS 72 Query: 215 LLFGAP-------VHWE-MPELKGFNFVGGWVLIPELL-----------ALTLALTVYTA 255 L G P +H+ MP L N GG +L +L + LA+T+ + Sbjct: 73 FLRGTPLFVQILLIHFALMPML--INPSGGLILSGDLAREIRSHYGAFASAVLAITLNSG 130 Query: 256 AFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVIIPPLTSQYLNLAKNS 315 A+++EI R+GI+S+ GQ+EA+RSLG+ TLR+V++PQA R ++PPL + + + K+S Sbjct: 131 AYVSEIFRAGIQSIDRGQSEASRSLGMSYLATLRRVVLPQAFRRMLPPLGNNAIAIVKDS 190 Query: 316 SLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISLLMNWYNKR 369 SLA+ IG E+ + A TV + E +Y I++++S L+ R Sbjct: 191 SLASAIGLAEL-AYAARTVSGAYARYWEPYLTISVIYWLITLALSALVRHLEAR 243 Score = 33.9 bits (76), Expect = 5e-06 Identities = 24/85 (28%), Positives = 36/85 (42%), Gaps = 10/85 (11%) Query: 62 YARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQN----------WIISKLATVYVE 111 Y +F+ G TL I VI T G ++GV RL++ + + YV Sbjct: 13 YLPLFVEGTWMTLKAAIICVIAGTCWGLVLGVGRLAEARHGFWKYFLCYCVQWPIRFYVS 72 Query: 112 VFRNIPPLLQILFWYFAVFLSMPGP 136 R P +QIL +FA+ + P Sbjct: 73 FLRGTPLFVQILLIHFALMPMLINP 97 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: 205 Number of extensions: 6 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: 250 Length adjustment: 27 Effective length of query: 348 Effective length of database: 223 Effective search space: 77604 Effective search space used: 77604 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