Align Serine transporter (characterized)
to candidate BWI76_RS23460 BWI76_RS23460 hypothetical protein
Query= SwissProt::P0AAD6 (429 letters) >FitnessBrowser__Koxy:BWI76_RS23460 Length = 409 Score = 305 bits (782), Expect = 1e-87 Identities = 164/415 (39%), Positives = 260/415 (62%), Gaps = 16/415 (3%) Query: 18 WRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILAFPMTFFAHRGLTRFVLS 77 W K +T+W LYGTA+GAG LFLPI G G I L I A++A+P+T++ H+ L++F+LS Sbjct: 5 WSKEETLWSFALYGTAVGAGTLFLPIQLGSAGAIVLFITALVAWPLTYWPHKALSQFILS 64 Query: 78 GK-NPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAITNTVESFMSHQLGMTP 136 PGE IT V ++G G LIT LYF A + ++L+Y+VAITN++ +S + +T Sbjct: 65 ANIAPGEGITGAVNHYYGKKIGSLITGLYFLAFFVVVLIYAVAITNSLAEQLSRHVPITS 124 Query: 137 PPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLALYLIPQWNGAALETLS 196 RA+LSL +++ + I G ++ +K M LVFP + + L++YL+ W A L T Sbjct: 125 QVRALLSLAVVLVLNLIFLMGRRVTIKVMGFLVFPLIACFLFLSIYLMGSWQPAYL-TSQ 183 Query: 197 LDTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYGDMAEQKCSKILAFAHI 256 + T + +W++IPVMVF+F+H+PIIS+FA+ ++E+YG+ A KC KI+ A+ Sbjct: 184 MQLTPHT----FHQIWISIPVMVFAFSHTPIISTFAIDQQEKYGEQAMGKCKKIMKVAYT 239 Query: 257 MMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPVIAWMAP---IIAIIAI 313 ++ +V+FFVFSC+LS+ + A+ Q ++ILS L+ +P AW+A I+A++A+ Sbjct: 240 LICASVLFFVFSCLLSIPAGYIETARNQGVTILSALSMMPGSP--AWLAVTGIIVAVVAM 297 Query: 314 TKSFLGHYLGAREGFNGMVIKSLRGKG--KSIEINKLNRITALFMLVTTWIVATLNPSIL 371 +KSFLG Y G EG + +V SL G KS N+ ++ L + T+ V +NP+ + Sbjct: 298 SKSFLGTYFGVIEGASEIVKTSLAQAGIRKSRAFNR--AMSILLVSTLTFAVCFINPNAI 355 Query: 372 GMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAISAIFYS 426 MI + GP+IAMILF+MP + +P ++ Y + N +V+GL+ +S +F+S Sbjct: 356 SMIYAISGPLIAMILFIMPTLSTYLIPTLKPYRS-VGNFITLVVGLLCVSVMFFS 409 Lambda K H 0.328 0.140 0.416 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: 480 Number of extensions: 25 Number of successful extensions: 6 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: 429 Length of database: 409 Length adjustment: 32 Effective length of query: 397 Effective length of database: 377 Effective search space: 149669 Effective search space used: 149669 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: 50 (23.9 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