Align TctC aka STM2786, component of The tricarboxylate transporter, TctABC (characterized)
to candidate BWI76_RS20035 BWI76_RS20035 hypothetical protein
Query= TCDB::Q9FA46 (325 letters) >FitnessBrowser__Koxy:BWI76_RS20035 Length = 326 Score = 554 bits (1428), Expect = e-163 Identities = 275/326 (84%), Positives = 294/326 (90%), Gaps = 1/326 (0%) Query: 1 MKKQLLRTLTASILLMST-SVLAQEAPSRTECIAPAKPGGGFDLTCKLIQVSLLETGAIE 59 M LR L+A L + T S A EAPSRTECIAPAKPGGGFDLTCKLIQVSL+ETGAI+ Sbjct: 1 MNIPFLRHLSALALCLCTASAWAVEAPSRTECIAPAKPGGGFDLTCKLIQVSLMETGAIK 60 Query: 60 KPMRVTYMPGGVGAVAYNAIVAQRPGEPGTVVAFSGGSLLNLSQGKFGRYGVDDVRWLAS 119 KPMRVTYMPGGVGAVAYNAIVAQRPGEPGTVVAFSGGSLLNL+QGKFGRYGVDDVRWLAS Sbjct: 61 KPMRVTYMPGGVGAVAYNAIVAQRPGEPGTVVAFSGGSLLNLAQGKFGRYGVDDVRWLAS 120 Query: 120 VGTDYGMIAVRADSPWKTLKDLMTAMEKDPNSVVIGAGASIGSQDWMKSALLAQKANVDP 179 VGTDYGMIAVR DSPWK L M AMEK+P S+VIGAGASIGSQDWMK+ALLAQKANVDP Sbjct: 121 VGTDYGMIAVRTDSPWKNLPSFMAAMEKNPASIVIGAGASIGSQDWMKAALLAQKANVDP 180 Query: 180 HKMRYVAFEGGGEPVTALMGNHVQVVSGDLSEMVPYLGGDKIRVLAVFSENRLPGQLANI 239 HKMRYVAFEGGGEPVTAL+GNHVQ VSGDLSEMVPYL G+KIRVLAVF+ RLPG LAN+ Sbjct: 181 HKMRYVAFEGGGEPVTALLGNHVQAVSGDLSEMVPYLQGNKIRVLAVFANERLPGALANV 240 Query: 240 PTAKEQGYDLVWPIIRGFYVGPKVSDADYQWWVDTFKKLQQTDEFKKQRDLRGLFEFDMT 299 PTAKEQGYDLVWPIIRGF+VGPKVSDADYQWWVD F KLQQTD FKKQR+LRGLFEF+M Sbjct: 241 PTAKEQGYDLVWPIIRGFFVGPKVSDADYQWWVDEFTKLQQTDAFKKQRELRGLFEFNMN 300 Query: 300 GQQLDDYVKKQVTDYREQAKAFGLAK 325 G++LD YVKKQV YR+QAK+FGLAK Sbjct: 301 GKELDAYVKKQVEAYRQQAKSFGLAK 326 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: 496 Number of extensions: 13 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: 325 Length of database: 326 Length adjustment: 28 Effective length of query: 297 Effective length of database: 298 Effective search space: 88506 Effective search space used: 88506 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: 48 (23.1 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