Align L-alanine and D-alanine permease (characterized)
to candidate PP_0927 PP_0927 aromatic amino acid transport protein
Query= reanno::WCS417:GFF1065 (472 letters) >FitnessBrowser__Putida:PP_0927 Length = 453 Score = 399 bits (1026), Expect = e-116 Identities = 202/450 (44%), Positives = 292/450 (64%), Gaps = 6/450 (1%) Query: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77 L+R L RHI+L+ALG IG GLFLG A+ I++AGP+++L Y I GL +IMR LGEM Sbjct: 10 LQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGPSVLLGYAIAGLMAFLIMRQLGEMV 69 Query: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFPDTPRWIW 137 V PVAGSFS +A Y AGF++GWNYW ++++ +AE+TAV +Y+ W+PD P W Sbjct: 70 VEEPVAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYWWPDFPTWAT 129 Query: 138 ALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197 A + + INL VK +GE EFWFAL+K+V I++M+ G G G G+ G ++N Sbjct: 130 AAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVSMI--GFGAWLLGSGHGGPDASVAN 187 Query: 198 LWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSVFWRILLF 257 LW +GGF PNGV G++M+L ++MF++ G+E++G+TA EA NP+++IP A V +RIL+F Sbjct: 188 LWQYGGFFPNGVTGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKATNQVVYRILIF 247 Query: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317 Y+GAL V+LS+YPW ++ GSPFVM F L A I+N VV+TAALS N +++ Sbjct: 248 YIGALAVLLSLYPWQKVVQGGSPFVMIFHELDSDLVATILNIVVLTAALSVYNSCVYANS 307 Query: 318 RMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLVPEKVFVWVTSIATF 377 RML+ LA G AP K S +GVP AL +S FA L VL+NYL+P F + ++A Sbjct: 308 RMLFGLASQGDAPRQLLKVSRSGVPLTALAVSAFATGLCVLINYLMPGGAFGLLMALAVS 367 Query: 378 GAIWTWLMILLAQLKFRKSLSPAEQAGLKYRMWLYPVSSYLALAFLLLVVGLMAYFPDTR 437 + W I + LKFRK+ A Y+ +P+++YL LAF++L++ +M P R Sbjct: 368 ALVINWASISITHLKFRKAKLAAGITPF-YKSLGHPLTNYLCLAFIVLILVVMYLTPPIR 426 Query: 438 IALYVGPVFLVLLTVLFYVFKLQPTQVAQG 467 I++ + P + + VL+ FKL+ + A+G Sbjct: 427 ISVMLIPAW---IAVLWVAFKLKKARQAKG 453 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: 647 Number of extensions: 28 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: 453 Length adjustment: 33 Effective length of query: 439 Effective length of database: 420 Effective search space: 184380 Effective search space used: 184380 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