Align TctC aka STM2786, component of The tricarboxylate transporter, TctABC (characterized)
to candidate WP_090447895.1 BLS63_RS21760 tripartite tricarboxylate transporter substrate binding protein
Query= TCDB::Q9FA46 (325 letters) >NCBI__GCF_900100495.1:WP_090447895.1 Length = 325 Score = 395 bits (1014), Expect = e-114 Identities = 190/325 (58%), Positives = 237/325 (72%) Query: 1 MKKQLLRTLTASILLMSTSVLAQEAPSRTECIAPAKPGGGFDLTCKLIQVSLLETGAIEK 60 MK R A+ L L P R ECIAPAKPGGGFDLTCKL Q L + G ++ Sbjct: 1 MKTAFTRIALATACLAFAGQLLAAEPKRPECIAPAKPGGGFDLTCKLAQTGLKDEGLLKA 60 Query: 61 PMRVTYMPGGVGAVAYNAIVAQRPGEPGTVVAFSGGSLLNLSQGKFGRYGVDDVRWLASV 120 PMRVTYMPGGVGAVAYNA+VAQR +PGT+ AFS GSLLNL+QGKFGRY + VRWLA+V Sbjct: 61 PMRVTYMPGGVGAVAYNAVVAQRAKDPGTITAFSSGSLLNLAQGKFGRYDENAVRWLAAV 120 Query: 121 GTDYGMIAVRADSPWKTLKDLMTAMEKDPNSVVIGAGASIGSQDWMKSALLAQKANVDPH 180 GTDYG I VRADSP++ L DL+ A++KDP+S+V GAGA+IG QDWM++AL+A+ A +DP Sbjct: 121 GTDYGAITVRADSPYQNLDDLVQALKKDPSSIVFGAGATIGGQDWMQTALIARLAGIDPK 180 Query: 181 KMRYVAFEGGGEPVTALMGNHVQVVSGDLSEMVPYLGGDKIRVLAVFSENRLPGQLANIP 240 +RYVAFEGGGE +TA++G HVQV S L E+ P L K+R+LAV S+ RLPG+LA++P Sbjct: 181 NLRYVAFEGGGETLTAMLGGHVQVTSSGLGEVTPQLEAKKVRILAVLSDERLPGKLADLP 240 Query: 241 TAKEQGYDLVWPIIRGFYVGPKVSDADYQWWVDTFKKLQQTDEFKKQRDLRGLFEFDMTG 300 TAKEQGYD+ WP+IRGFY+GP+VSD + WW F L +++F K R R L MTG Sbjct: 241 TAKEQGYDITWPVIRGFYMGPEVSDEQFNWWKQQFDTLLASEDFAKLRAQRDLQPLAMTG 300 Query: 301 QQLDDYVKKQVTDYREQAKAFGLAK 325 +L +V KQV +Y+ A FGL + Sbjct: 301 DELKTFVFKQVEEYKALAGEFGLVQ 325 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: 401 Number of extensions: 12 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: 325 Length adjustment: 28 Effective length of query: 297 Effective length of database: 297 Effective search space: 88209 Effective search space used: 88209 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 24 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