Align TctC aka STM2786, component of The tricarboxylate transporter, TctABC (characterized)
to candidate BPHYT_RS11030 BPHYT_RS11030 transporter
Query= TCDB::Q9FA46 (325 letters) >FitnessBrowser__BFirm:BPHYT_RS11030 Length = 332 Score = 133 bits (334), Expect = 7e-36 Identities = 92/280 (32%), Positives = 141/280 (50%), Gaps = 15/280 (5%) Query: 14 LLMSTSVLAQEA----PSRT-ECIAPAKPGGGFDLTCKLIQVSLLETGAIEKPMRVTYMP 68 LL + + LA A P R E + P+ PGGG DL + +Q + + KP+ V P Sbjct: 18 LLAACATLANAADAWQPRRPIEIVVPSAPGGGLDLVARTLQSVIQQEKLSAKPVTVINRP 77 Query: 69 GGVGAVAYNAIVAQRPGEPGTVVAFSGGSLLNLSQGKFGRYGVDDVRWLASVGTDYGMIA 128 GG G V+ I + G V L+ G+DDV LA T+ + + Sbjct: 78 GGGGTVSIAYINSHEAD--GHFVTVQALPLITNRITGLSTVGIDDVTPLAVFVTEQVVFS 135 Query: 129 VRADSPWKTLKDLMTAMEKDPNSVVIGAGASIGSQDWMKSALLAQKANVDPHKMRYVAFE 188 V +SP K+ DL+ ++KDP SV +G +S G Q +AL+ + A DP KM+ V F+ Sbjct: 136 VPGNSPIKSGSDLVQMLKKDPTSVTLGVSSSPGGQSHDAAALVMKGAGQDPKKMKVVFFD 195 Query: 189 GGGEPVTALMGNHVQVVSGDLSEMVPYLGGDKIRVLAVFSENRLPGQLANIPTAKEQGYD 248 GGE +TALMG HV + ++ +R++A+ R G+LAN+PT KEQG + Sbjct: 196 SGGEALTALMGGHVTASATPAGVVLGPSKSGSVRMIAIPGGARQGGELANVPTWKEQGIN 255 Query: 249 L---VWPIIRGFYVGPK-VSDADYQWWVDTFKKLQQTDEF 284 + W ++ VGPK ++ A+ WW + +K + E+ Sbjct: 256 VDFTTWRVL----VGPKNMTPAEIAWWDNVLQKATASPEW 291 Lambda K H 0.318 0.135 0.401 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: 323 Number of extensions: 14 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 325 Length of database: 332 Length adjustment: 28 Effective length of query: 297 Effective length of database: 304 Effective search space: 90288 Effective search space used: 90288 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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