Align D-alanine and L-alanine transporter (characterized)
to candidate Pf6N2E2_1423 Gamma-aminobutyrate permease
Query= reanno::pseudo3_N2E3:AO353_16120 (472 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1423 Length = 466 Score = 298 bits (763), Expect = 3e-85 Identities = 164/439 (37%), Positives = 258/439 (58%), Gaps = 11/439 (2%) Query: 16 GPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGE 75 G L + RH+ ++++ IG GLF+GS AI AGPA+ML+Y+ GL ++++MR LGE Sbjct: 11 GHLAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGPAVMLAYLFSGLLVVLVMRMLGE 70 Query: 76 MAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPEVPRW 135 MAV NP GSFS YA +G AGF GW YW+ W++ E A + WFP + W Sbjct: 71 MAVANPDTGSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEALAAGHVLNQWFPAIDAW 130 Query: 136 IWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVVGGVGVIAFGFGNDGVALGI 195 ++A ++V + NL +V +GEFEFWFA+ K+V II + G V+ G+ + A G+ Sbjct: 131 LFASVSIVLLAVTNLFSVSKYGEFEFWFAMAKVVAIIGFISLGFAVL-MGWIPEREASGL 189 Query: 196 SNLW-SHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRI 254 S L HGGF PNG+ V+ + +MF+++G E + + A E+ NP + I A SV WRI Sbjct: 190 SRLMEEHGGFAPNGLSAVVGAFITIMFSFIGTEAVTIAAAESDNPAQNIAKATRSVIWRI 249 Query: 255 LLFYVGALFVILSIYPWNE--IGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGG 312 +FY+ ++FV++S+ PWN+ + + GS + E + I A +++ VV+ A S N Sbjct: 250 GVFYLLSIFVVISVVPWNDPLLASVGS-YQRALELMNIPHAKFLVDMVVLIAVASCMNSS 308 Query: 313 IFSTGRMLYSLAQNGQAPAGFAKTSN-GVPRRALLLSIGALLLGV-LLNYLVPEKVFVWV 370 I+ RMLYSL + G AP TS+ GVPR A++ S L GV L +Y +P +F ++ Sbjct: 309 IYIASRMLYSLGRRGDAPKALKVTSSAGVPRSAVIAST-VLGAGVTLFSYFMPAGLFQFL 367 Query: 371 TAIATFGAIWTWVMILLAQLKFRKGLSPAERAALKYRMWLYPVSSYLALAFLVMVVGLMA 430 A + A+ +++I ++QL+ R+ L + L +RMWL+P ++L + F+ + +M Sbjct: 368 LASSGAIALLVYLVIAISQLRMRRMLQ-RQNIELPFRMWLFPWLTWLVIVFISAALAVMM 426 Query: 431 YFPDTR--VALYVGPAFLV 447 P+ R V+ +G A ++ Sbjct: 427 VTPEHRSEVSTTLGLALVI 445 Lambda K H 0.328 0.142 0.446 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: 658 Number of extensions: 47 Number of successful extensions: 4 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: 472 Length of database: 466 Length adjustment: 33 Effective length of query: 439 Effective length of database: 433 Effective search space: 190087 Effective search space used: 190087 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: 51 (24.3 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