Align TctC aka STM2786, component of The tricarboxylate transporter, TctABC (characterized)
to candidate GFF205 Psest_0206 Uncharacterized protein conserved in bacteria
Query= TCDB::Q9FA46 (325 letters) >FitnessBrowser__psRCH2:GFF205 Length = 324 Score = 408 bits (1048), Expect = e-118 Identities = 201/326 (61%), Positives = 247/326 (75%), Gaps = 3/326 (0%) Query: 1 MKKQLLR-TLTASILLMSTSVLAQEAPSRTECIAPAKPGGGFDLTCKLIQVSLLETGAIE 59 MK +L R L +S LL+S+ +LA+ P R ECIAPAKPGGGFDLTCKL Q L + G ++ Sbjct: 1 MKTRLSRIALLSSCLLLSSQLLAE--PKRPECIAPAKPGGGFDLTCKLAQSGLKDAGLLK 58 Query: 60 KPMRVTYMPGGVGAVAYNAIVAQRPGEPGTVVAFSGGSLLNLSQGKFGRYGVDDVRWLAS 119 PMRVTYMPGGVGAVAYNA+VAQR E GT+ AFS GSLLNL+QGKFGRY VRWLA+ Sbjct: 59 APMRVTYMPGGVGAVAYNAVVAQRAAEAGTITAFSSGSLLNLAQGKFGRYDESAVRWLAA 118 Query: 120 VGTDYGMIAVRADSPWKTLKDLMTAMEKDPNSVVIGAGASIGSQDWMKSALLAQKANVDP 179 VGTDYG I+VRAD+P++ L +L+ A++KDP SVV GAGA+IG QDWM++AL+A+ A VDP Sbjct: 119 VGTDYGAISVRADAPYQNLDELIAAVKKDPGSVVFGAGATIGGQDWMQTALIARAAGVDP 178 Query: 180 HKMRYVAFEGGGEPVTALMGNHVQVVSGDLSEMVPYLGGDKIRVLAVFSENRLPGQLANI 239 K+RYVAFEGGGE +TA++G HVQV S L E+ P L KIR+LAV S+ RLPG+L I Sbjct: 179 QKLRYVAFEGGGETLTAMLGGHVQVTSSGLGEVTPQLDAGKIRILAVLSDERLPGKLNGI 238 Query: 240 PTAKEQGYDLVWPIIRGFYVGPKVSDADYQWWVDTFKKLQQTDEFKKQRDLRGLFEFDMT 299 PTAKEQGYD+ WP+IRGFY+GP+VSD D+ WW F L ++F K R+ R LF MT Sbjct: 239 PTAKEQGYDISWPVIRGFYMGPEVSDEDFNWWKTQFDTLLGDEDFAKLREQRDLFPLSMT 298 Query: 300 GQQLDDYVKKQVTDYREQAKAFGLAK 325 G +L +V+KQV DY+ A FGL K Sbjct: 299 GDELKAFVEKQVQDYKALAGEFGLVK 324 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: 391 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: 324 Length adjustment: 28 Effective length of query: 297 Effective length of database: 296 Effective search space: 87912 Effective search space used: 87912 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