Align Serine transporter (characterized)
to candidate BWI76_RS14475 BWI76_RS14475 serine/threonine transporter
Query= SwissProt::P0AAD6 (429 letters) >FitnessBrowser__Koxy:BWI76_RS14475 Length = 427 Score = 752 bits (1941), Expect = 0.0 Identities = 382/429 (89%), Positives = 405/429 (94%), Gaps = 2/429 (0%) Query: 1 METTQTSTIASKDSRSAWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILA 60 MET Q + +A + S WRK+DT+WMLGLYGTAIGAGVLFLPINAGVGG+IPLIIMAILA Sbjct: 1 METVQNTLVARESS--GWRKSDTVWMLGLYGTAIGAGVLFLPINAGVGGLIPLIIMAILA 58 Query: 61 FPMTFFAHRGLTRFVLSGKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAI 120 FPMTFFAHRGLTRFVLSGKNPGEDITEVVEEHFG GAGKLITLLYFFAIYPILLVYSVAI Sbjct: 59 FPMTFFAHRGLTRFVLSGKNPGEDITEVVEEHFGTGAGKLITLLYFFAIYPILLVYSVAI 118 Query: 121 TNTVESFMSHQLGMTPPPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLA 180 TNTV+SF++HQLG+ PPRAILSLILIVGMM IVRFGE+MIVKAMS+LVFPFV LM+LA Sbjct: 119 TNTVDSFITHQLGLVSPPRAILSLILIVGMMGIVRFGEKMIVKAMSVLVFPFVFALMILA 178 Query: 181 LYLIPQWNGAALETLSLDTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYG 240 LYLIPQWNGA L+TLSL ASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYG Sbjct: 179 LYLIPQWNGAVLDTLSLSGASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYG 238 Query: 241 DMAEQKCSKILAFAHIMMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPV 300 + AE+KCS+IL FAHIMMVLTVMFFVFSCVLSL+P +LA AK QNISILSYLANHFNAPV Sbjct: 239 EDAERKCSRILGFAHIMMVLTVMFFVFSCVLSLSPENLAEAKAQNISILSYLANHFNAPV 298 Query: 301 IAWMAPIIAIIAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTT 360 IAWMAPIIA+IAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLN+ITALFMLVTT Sbjct: 299 IAWMAPIIAMIAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNKITALFMLVTT 358 Query: 361 WIVATLNPSILGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAI 420 WIVATLNPSILGMIETLGGP+IAMILFLMPMYAI KVPAMRKYSGHISN FVVVMGLIAI Sbjct: 359 WIVATLNPSILGMIETLGGPVIAMILFLMPMYAINKVPAMRKYSGHISNAFVVVMGLIAI 418 Query: 421 SAIFYSLFS 429 SAIF+SLFS Sbjct: 419 SAIFFSLFS 427 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: 816 Number of extensions: 31 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: 429 Length of database: 427 Length adjustment: 32 Effective length of query: 397 Effective length of database: 395 Effective search space: 156815 Effective search space used: 156815 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