Align Proline-specific permease (ProY) (characterized)
to candidate PP_1059 PP_1059 Uncharacterized amino acid permease YtnA
Query= TCDB::P37460 (456 letters) >FitnessBrowser__Putida:PP_1059 Length = 472 Score = 524 bits (1350), Expect = e-153 Identities = 247/435 (56%), Positives = 330/435 (75%) Query: 7 LKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRALGEMS 66 LKR L RHIR MALG+ IG GLF GSA AI+MAGP+++L+YIIGG+A +IMRALGEM+ Sbjct: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77 Query: 67 VHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAVPHWIW 126 VHNP A SFSRYAQ+ LGPLAG++TGW Y F L+ +A++TA IYMG+WFP VP WIW Sbjct: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAIYMGIWFPDVPRWIW 137 Query: 127 VLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQPTGIHN 186 L+ + + A+NL++VK FGE EFWF+ K+ TII M++ GIGII +G GN G GI N Sbjct: 138 ALAALGSMGAVNLVAVKAFGEFEFWFALIKIVTIIAMVLGGIGIIAFGFGNDGVAVGISN 197 Query: 187 LWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILVF 246 LWSNGGF NG G++MSLQMVMFAY G+E+IG+TAGEA++P+K+IP+AI SV RIL+F Sbjct: 198 LWSNGGFMPNGVTGVLMSLQMVMFAYLGVEMIGLTAGEARNPQKTIPQAIGSVFWRILLF 257 Query: 247 YVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDVFGVG 306 YVG LFVI+SIYPWN++G+ GSPFV+TF+ +GI AA I+NFVV+TA+LS+ N +F G Sbjct: 258 YVGALFVILSIYPWNEIGSQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317 Query: 307 RMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVIASLATF 366 RML+ +A+ G AP FA+TS+ G+P +L+ ALL V NY++PE VF+ + S+ATF Sbjct: 318 RMLYSLAQNGQAPAAFARTSKNGVPRNALLLSIGALLLGVLANYLVPEKVFVWVTSIATF 377 Query: 367 ATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIGYHPDTR 426 +W W+MILL+Q+ FR L E KALK+++ +++ L FLV ++ L+ Y DTR Sbjct: 378 GAIWTWVMILLAQLKFRAGLTTAERKALKYRMWLWPLSSYLALAFLVLVVGLMAYFEDTR 437 Query: 427 ISLYVGFAWIVLLLI 441 ++LY+G A++VLL + Sbjct: 438 VALYIGPAFLVLLTV 452 Lambda K H 0.329 0.143 0.449 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: 705 Number of extensions: 33 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: 456 Length of database: 472 Length adjustment: 33 Effective length of query: 423 Effective length of database: 439 Effective search space: 185697 Effective search space used: 185697 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: 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