Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate GFF195 PGA1_c01990 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >FitnessBrowser__Phaeo:GFF195 Length = 410 Score = 288 bits (737), Expect = 2e-82 Identities = 166/389 (42%), Positives = 234/389 (60%), Gaps = 17/389 (4%) Query: 2 RAWVFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEADS 61 R+ FQ + + + W+L +N NL+ G+ +GFL +G+ I Q LI+Y S Sbjct: 24 RSLTFQAIAALVLALAIWYLGNNLIQNLRAAGLNISYGFLGDPSGYDINQRLIEYDSQSS 83 Query: 62 YARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQ 121 +AR ++G+LNTLLV + I ATI G + GV RLS NW++SKL VYVE+FRNIP L+ Sbjct: 84 HARAAVVGVLNTLLVAVLACITATIFGVVAGVLRLSNNWLVSKLMAVYVEIFRNIPVLIW 143 Query: 122 ILFWYFAVFLSMPGPR-------AAHNFGDTFFVSSRGLNMPAALVAEGFWPFV----IS 170 I+ + + MPGPR + D F ++RG+ +P GF+ + Sbjct: 144 IIIIFTIMTAVMPGPREFRGDNATSSMLFDLFAFTNRGVYIPMPWFESGFFASGALNWLV 203 Query: 171 VVLAIVAIVLMTRW----ANKRFEATGEPFHKFWVGLALFLVIPALSALLFGAPVHWEMP 226 V+ A+V L+ R A K E TG + L ++LV L+ +LF + WE+P Sbjct: 204 VIAALVGSFLVMRRIEANATKTQEKTGVRPKTKLIALGVWLV--PLALVLFVMGLSWEVP 261 Query: 227 ELKGFNFVGGWVLIPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGP 286 ELKGFNF GG + L+AL AL++YT AFIAE VR+GI++++ GQTEAA +LGLR G Sbjct: 262 ELKGFNFKGGIKIGGPLIALWFALSIYTGAFIAENVRAGIQAINKGQTEAAAALGLRPGR 321 Query: 287 TLRKVIIPQALRVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIA 346 + V++PQALRVIIPPL S +LN+ KNSSLA +GY ++ + G LNQTG+AIE + Sbjct: 322 IMNLVVLPQALRVIIPPLISNFLNITKNSSLAIAVGYADITATLGGITLNQTGRAIECVL 381 Query: 347 ITMSVYLAISISISLLMNWYNKRIALIER 375 + M YL S+ IS++MN YN + L ER Sbjct: 382 LLMLFYLTASLLISMVMNVYNASVKLKER 410 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: 408 Number of extensions: 24 Number of successful extensions: 2 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: 410 Length adjustment: 31 Effective length of query: 344 Effective length of database: 379 Effective search space: 130376 Effective search space used: 130376 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 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