Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate WP_086509148.1 BZY95_RS06445 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >NCBI__GCF_002151265.1:WP_086509148.1 Length = 396 Score = 443 bits (1140), Expect = e-129 Identities = 218/374 (58%), Positives = 286/374 (76%) Query: 2 RAWVFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEADS 61 RA +FQV+ + AV A ++ NTQ NL RGIT+GFGFL+R+AGFGI Q LI+Y+ + Sbjct: 23 RALLFQVLLIAAVAAFLLYIIGNTQDNLAARGITTGFGFLDRTAGFGIGQSLIEYSSQST 82 Query: 62 YARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQ 121 Y R F++GLLNTLLV+ +GVI ATI+GFI+G+ARLS NW+I++LA+ Y+E+FRNIP LLQ Sbjct: 83 YGRTFVVGLLNTLLVSALGVIAATIIGFIVGIARLSPNWLIARLASGYIEIFRNIPLLLQ 142 Query: 122 ILFWYFAVFLSMPGPRAAHNFGDTFFVSSRGLNMPAALVAEGFWPFVISVVLAIVAIVLM 181 I FWYFAV +MP R +++ G+ F++ RGL +P L GF ++ V+AIVA + + Sbjct: 143 IFFWYFAVLRAMPAARDSYSLGEVIFLNVRGLYLPEPLFESGFGLIPLTFVVAIVASIAL 202 Query: 182 TRWANKRFEATGEPFHKFWVGLALFLVIPALSALLFGAPVHWEMPELKGFNFVGGWVLIP 241 W +R EATG+ W+ LAL L +P L + G PV W++PEL+GFNF GG +IP Sbjct: 203 VIWNKRRHEATGKRLPAGWISLALILGLPMLVLVATGVPVTWDVPELRGFNFRGGITIIP 262 Query: 242 ELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVII 301 E LAL LAL++YTA+FIAEIVRSGI+++ HGQTEAA++L L LR V++PQALRVII Sbjct: 263 EFLALWLALSIYTASFIAEIVRSGIQAIPHGQTEAAQALSLPQKLVLRLVVVPQALRVII 322 Query: 302 PPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISL 361 PPLTSQYLNL KNSSLA IGYP++VS+FAGT LNQTGQAIEVI++TM+VYL IS+ +S+ Sbjct: 323 PPLTSQYLNLIKNSSLATAIGYPDLVSVFAGTTLNQTGQAIEVISMTMAVYLIISLLVSM 382 Query: 362 LMNWYNKRIALIER 375 MNW+N R+AL+ER Sbjct: 383 FMNWFNARVALVER 396 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: 513 Number of extensions: 18 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 375 Length of database: 396 Length adjustment: 30 Effective length of query: 345 Effective length of database: 366 Effective search space: 126270 Effective search space used: 126270 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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