Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate BWI76_RS23460 BWI76_RS23460 hypothetical protein
Query= SwissProt::P0AAD8 (443 letters) >FitnessBrowser__Koxy:BWI76_RS23460 Length = 409 Score = 229 bits (583), Expect = 2e-64 Identities = 136/421 (32%), Positives = 229/421 (54%), Gaps = 24/421 (5%) Query: 17 WRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYPIAFYCHRALARLCLS 76 W K +T W+ L+GTA+GAG LF PI+ G G I + + ++A+P+ ++ H+AL++ LS Sbjct: 5 WSKEETLWSFALYGTAVGAGTLFLPIQLGSAGAIVLFITALVAWPLTYWPHKALSQFILS 64 Query: 77 GS-NPSGNITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITNTFMTFWENQLGFAP 135 + P IT V ++GK G +IT LYF A ++ IY V ITN+ + Sbjct: 65 ANIAPGEGITGAVNHYYGKKIGSLITGLYFLAFFVVVLIYAVAITNSLAEQLSRHVPITS 124 Query: 136 LNRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLSLIPYWNSAVIDQVD 195 R ++L ++L++ + G+ + +KVM +LV+P IA + +S+ L+ W A + Sbjct: 125 QVRALLSLAVVLVLNLIFLMGRRVTIKVMGFLVFPLIACFLFLSIYLMGSWQPAYL---- 180 Query: 196 LGSLSLTGHDGILITVWLGISIMVFSFNFSPIVSSFVVSKREEY-EKDFGRDFTERKCSQ 254 + LT H +W+ I +MVF+F+ +PI+S+F + ++E+Y E+ G KC + Sbjct: 181 TSQMQLTPH--TFHQIWISIPVMVFAFSHTPIISTFAIDQQEKYGEQAMG------KCKK 232 Query: 255 IISRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLANHFASMTGTKTTFAIT 314 I+ A L+ A V+FF FSCL ++ + A+ Q + +LS L + M G+ A+T Sbjct: 233 IMKVAYTLICASVLFFVFSCLLSIPAGYIETARNQGVTILSAL----SMMPGSPAWLAVT 288 Query: 315 LEYAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYKGDKTKVSLGKLNTISMIFIMGS 374 I+A+VA+ KSF G Y G +EG + +V K + S +S++ + Sbjct: 289 ----GIIVAVVAMSKSFLGTYFGVIEGASEIV-KTSLAQAGIRKSRAFNRAMSILLVSTL 343 Query: 375 TWVVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYRGRLDNVFVTVIGLLT 434 T+ V + NPN + +I A+ P+IA +L ++P + P+L YR + N V+GLL Sbjct: 344 TFAVCFINPNAISMIYAISGPLIAMILFIMPTLSTYLIPTLKPYRS-VGNFITLVVGLLC 402 Query: 435 I 435 + Sbjct: 403 V 403 Lambda K H 0.328 0.141 0.430 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: 505 Number of extensions: 23 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: 443 Length of database: 409 Length adjustment: 32 Effective length of query: 411 Effective length of database: 377 Effective search space: 154947 Effective search space used: 154947 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