Align L-alanine and D-alanine permease (characterized)
to candidate GFF344 PS417_01755 proline-specific permease
Query= reanno::pseudo5_N2C3_1:AO356_17670 (473 letters) >FitnessBrowser__WCS417:GFF344 Length = 469 Score = 519 bits (1336), Expect = e-152 Identities = 245/439 (55%), Positives = 327/439 (74%), Gaps = 2/439 (0%) Query: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77 LKR L RHIR MALG+ IG GLF GSA AI+MAGPA++L+Y+IGG A+ ++MRALGEMA Sbjct: 8 LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMA 67 Query: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137 VHNPVAGSF +YA YLGP+AGF+ GW Y F ++ C+A++TA +YMG WFPDV RW+W Sbjct: 68 VHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMIIVCLADVTAFGIYMGFWFPDVARWVW 127 Query: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGV--ALGI 195 L ++ +G +NL VK FGE EFW +L+K+ I+AM++GG GI+ FG + G A G+ Sbjct: 128 VLGIVLLIGGLNLCNVKVFGEMEFWLSLLKVGAIVAMILGGFGIMLFGIHSAGETQASGL 187 Query: 196 SNLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRIL 255 SNLWAHGGFMPNG+ G++ S +VMFA+ G+E+IG+TAGEAK+PQ+ IP AI +V RIL Sbjct: 188 SNLWAHGGFMPNGIGGLIASFAVVMFAFGGIEIIGITAGEAKDPQRVIPKAINAVPLRIL 247 Query: 256 LFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFS 315 LFYV LFV+++IYPW +IG+QGSPFV F LGI +AA I+N VVI+AA+S+ N IF Sbjct: 248 LFYVLTLFVLMAIYPWPQIGSQGSPFVQIFSNLGIGSAATILNIVVISAAVSAINSDIFG 307 Query: 316 TGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSIA 375 GRM+Y LAQ GQAP GFA+ S GVP +++ AALL GV+LNYL+PE VF+ + SIA Sbjct: 308 AGRMMYGLAQQGQAPKGFAQLSKQGVPWMTVVVMGAALLGGVVLNYLIPENVFLVIASIA 367 Query: 376 TFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFPD 435 TF +W W+MIL Q+ R+S++ + A LK+ + +P + A+ F++ V G++ YFPD Sbjct: 368 TFATVWVWLMILFTQVAMRRSMTKEQVAELKFPVPFWPYAPAAAIVFMLFVFGVLGYFPD 427 Query: 436 TRVALYVGPAFLVLLTVLF 454 T+ AL VG ++VLL V + Sbjct: 428 TQAALLVGAVWIVLLVVAY 446 Lambda K H 0.328 0.142 0.444 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: 752 Number of extensions: 40 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: 473 Length of database: 469 Length adjustment: 33 Effective length of query: 440 Effective length of database: 436 Effective search space: 191840 Effective search space used: 191840 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