Align L-alanine and D-alanine permease (characterized)
to candidate 14540 b0402 predicted cryptic proline transporter (NCBI)
Query= reanno::WCS417:GFF1065 (472 letters) >FitnessBrowser__Keio:14540 Length = 457 Score = 526 bits (1354), Expect = e-154 Identities = 248/451 (54%), Positives = 335/451 (74%) Query: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77 LKR L RHIR MALG+ IG GLF GSA AI+MAGP+++L+YIIGG+A +IMRALGEM+ Sbjct: 7 LKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGIAAYIIMRALGEMS 66 Query: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFPDTPRWIW 137 VHNP A SFSRYAQ+ LGPLAG++TGW Y F L+ +A++TA +YMGVWFP P WIW Sbjct: 67 VHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPTVPHWIW 126 Query: 138 ALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197 L+ ++ + ++NL++VK FGE EFWF+ K+ TII M++ G GII +G GN G GI N Sbjct: 127 VLSVVLIICAVNLMSVKVFGELEFWFSFFKVATIIIMIVAGFGIIIWGIGNGGQPTGIHN 186 Query: 198 LWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSVFWRILLF 257 LW++GGF NG G++MSLQMVMFAY G+E+IG+TAGEAK+P+K+IP AI SV RIL+F Sbjct: 187 LWSNGGFFSNGWLGMVMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILVF 246 Query: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317 YVG LFVI+SIYPWN++GT GSPFV+TF+ +GI AA I+NFVV+TA+LS+ N +F G Sbjct: 247 YVGTLFVIMSIYPWNQVGTAGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDVFGVG 306 Query: 318 RMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLVPEKVFVWVTSIATF 377 RML+ +A+ G AP F+KTS G+P +L+ ALL V LNY++PE VF+ + S+ATF Sbjct: 307 RMLHGMAEQGSAPKIFSKTSRRGIPWVTVLVMTTALLFAVYLNYIMPENVFLVIASLATF 366 Query: 378 GAIWTWLMILLAQLKFRKSLSPAEQAGLKYRMWLYPVSSYLALAFLLLVVGLMAYFPDTR 437 +W W+MILL+Q+ FR+ L P E LK+++ ++ L FLL ++GL+ Y PDTR Sbjct: 367 ATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVATTIGGLIFLLFIIGLIGYHPDTR 426 Query: 438 IALYVGPVFLVLLTVLFYVFKLQPTQVAQGE 468 I+LYVG ++V+L + + + Q+A+ + Sbjct: 427 ISLYVGFAWIVVLLIGWMFKRRHDRQLAENQ 457 Lambda K H 0.328 0.142 0.447 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: 715 Number of extensions: 36 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: 472 Length of database: 457 Length adjustment: 33 Effective length of query: 439 Effective length of database: 424 Effective search space: 186136 Effective search space used: 186136 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