Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate 16926 b2845 predicted transporter (NCBI)
Query= SwissProt::P0AAD8 (443 letters) >FitnessBrowser__Keio:16926 Length = 409 Score = 222 bits (566), Expect = 1e-62 Identities = 130/420 (30%), Positives = 227/420 (54%), Gaps = 22/420 (5%) Query: 17 WRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYPIAFYCHRALARLCLS 76 W K +T W+ L+GTA+GAG LF PI+ G G + + + ++A+P+ ++ H+AL + LS Sbjct: 5 WSKEETLWSFALYGTAVGAGTLFLPIQLGSAGAVVLFITALVAWPLTYWPHKALCQFILS 64 Query: 77 GSNPSG-NITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITNTFMTFWENQLGFAP 135 +G IT V ++GK G +IT LYF A ++ IY V ITN+ + Sbjct: 65 SKTSAGEGITGAVTHYYGKKIGNLITTLYFIAFFVVVLIYAVAITNSLTEQLAKHMVIDL 124 Query: 136 LNRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLSLIPYWNSAVIDQVD 195 R V+L ++L++ + G+ ++VM +LV+P IA + +S+ L+ W Q D Sbjct: 125 RIRMLVSLGVVLILNLIFLMGRHATIRVMGFLVFPLIAYFLFLSIYLVGSW------QPD 178 Query: 196 LGSLSLTGHDGILITVWLGISIMVFSFNFSPIVSSFVVSKREEYEKDFGRDFTERKCSQI 255 L + + + L +W+ I +MVF+F+ +PI+S+F + +RE+Y + KC +I Sbjct: 179 LLTTQVEFNQNTLHQIWISIPVMVFAFSHTPIISTFAIDRREKY-----GEHAMDKCKKI 233 Query: 256 ISRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLANHFASMTGTKTTFAITL 315 + A +++ V+FF FSCL ++ P+ + AK + + +LS L SM + L Sbjct: 234 MKVAYLIICISVLFFVFSCLLSIPPSYIEAAKEEGVTILSAL-----SMLPNAPAW---L 285 Query: 316 EYAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYKGDKTKVSLGKLNTISMIFIMGST 375 + I+A+VA+ KSF G Y G +EG V+K + K S +S++ + T Sbjct: 286 SISGIIVAVVAMSKSFLGTYFGVIEGATE-VVKTTLQQVGVKKSRAFNRALSIMLVSLIT 344 Query: 376 WVVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYRGRLDNVFVTVIGLLTI 435 ++V NPN + +I A+ P+IA +L ++P + P+L +R + N+ ++G+L + Sbjct: 345 FIVCCINPNAISMIYAISGPLIAMILFIMPTLSTYLIPALKPWRS-IGNLITLIVGILCV 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: 519 Number of extensions: 26 Number of successful extensions: 8 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