Align D-serine/D-alanine/glycine transporter (characterized)
to candidate BWI76_RS08745 BWI76_RS08745 proline-specific permease
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__Koxy:BWI76_RS08745 Length = 459 Score = 350 bits (897), Expect = e-101 Identities = 177/451 (39%), Positives = 282/451 (62%), Gaps = 10/451 (2%) Query: 19 LRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELL 78 L R L RHI+ IA+G AIGTGLF GS I AGP+++ Y+I G +F VMRA+GE+ Sbjct: 9 LLRGLNARHIRFIALGSAIGTGLFYGSASAIKAAGPAVLLAYLIGGAAVFIVMRALGEMA 68 Query: 79 LSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSDWVA 138 + N SFS +A LGP AG+ TGWTY F V+ +ADV A Y W+PD+ W+ Sbjct: 69 VRNPVSGSFSSYARQYLGPLAGFITGWTYTFEMVIVALADVTAFGIYMGLWYPDVPRWIW 128 Query: 139 SLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQS---PTGVEA 195 L++I + +NL +V++FGEMEFW ++IK+VAI+++IV G ++ F + TG+E Sbjct: 129 VLSIIFFIGAMNLCSVRVFGEMEFWLSLIKVVAIIAMIVAGGSIIFFGFGNAFPATGLE- 187 Query: 196 SFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIR 255 +LW+ GG+ P G G A I +FAF G+E++G TAAE K+P+K +P+AIN+IP+R Sbjct: 188 ---NLWSHGGFAPNGWEGIIASLGIVMFAFGGVEIIGVTAAEAKNPQKVIPQAINTIPLR 244 Query: 256 IIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGV 315 I++FYV L ++M++ PW+S SPFV +F +G+PAAA+++N +V++++ S+ NS + Sbjct: 245 IVLFYVCTLAILMAIFPWNSFGERGSPFVLIFDGLGIPAAATILNIIVISASISAINSDI 304 Query: 316 FSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMI 375 F RM++G+A+EG+APK+F +++ VP + + LL VV+ Y+ P + F +I Sbjct: 305 FGAGRMMYGMAKEGLAPKSFQRIASNGVPWMTVVVMGVALLAAVVLNYLMPEQV--FVLI 362 Query: 376 TTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSI-YKMPLGKLMCWVCMAFFVFVVVLLT 434 +++A ++VW +IL ++ R+ +I + +PL + + + F V+ +L Sbjct: 363 ASLAAFATVWVWVMILLAHFAMRRGLSAEERGNIAFPVPLWPVAPLLTLLFMGLVIAVLG 422 Query: 435 LEDDTRQALLVTPLWFIALGLGWLFIGKKRA 465 + ++TR AL+ +W L W +K A Sbjct: 423 MVEETRIALIAGLVWLGLLTAVWFARVRKNA 453 Lambda K H 0.329 0.141 0.440 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: 642 Number of extensions: 34 Number of successful extensions: 3 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: 470 Length of database: 459 Length adjustment: 33 Effective length of query: 437 Effective length of database: 426 Effective search space: 186162 Effective search space used: 186162 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