Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Echvi_1096 Echvi_1096 nitrate transport ATP-binding subunits C and D
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Cola:Echvi_1096 Length = 294 Score = 100 bits (248), Expect = 6e-26 Identities = 72/228 (31%), Positives = 127/228 (55%), Gaps = 17/228 (7%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 I+E++N++ + G SR+ ++D++ V +GE + I+G SGSGKTTLI+ +L + P Sbjct: 3 IIELNNVSKSFGMGASRV-DVLSDINLQVAEGEFVAIVGFSGSGKTTLIN-LLNGLAFPD 60 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164 + G+V+ +G + D R +++++ S +P S N L + E+F + Sbjct: 61 Q---GEVLLHGQPVTGPGPD--RGVIFQNYSLLPWLSVYN-NVKLAVDEVF-------PQ 107 Query: 165 ADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTS 224 K + + +V L PA + P +LSGGM+QRV +A +L +NP+++LMDEP S Sbjct: 108 LSSKEKASHIKKYIGMVNLTPA--MDKLPKELSGGMRQRVSVARALAMNPEILLMDEPLS 165 Query: 225 ALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKG 272 ALD L + L + I I + T + +T+D+ +A+R++ + G Sbjct: 166 ALDALTRGSLQEEIIRIWSQDKKTAILITNDVDEGILMADRIIPLTPG 213 Lambda K H 0.319 0.138 0.391 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: 240 Number of extensions: 10 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: 362 Length of database: 294 Length adjustment: 28 Effective length of query: 334 Effective length of database: 266 Effective search space: 88844 Effective search space used: 88844 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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