Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_011382778.1 AMB_RS01675 ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >NCBI__GCF_000009985.1:WP_011382778.1 Length = 275 Score = 99.8 bits (247), Expect = 8e-26 Identities = 78/235 (33%), Positives = 131/235 (55%), Gaps = 24/235 (10%) Query: 46 LEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGK 105 +EV NL Y G+ +I+ +DVS V +GEI+ I+G SGSGKTTL+S +L +P Sbjct: 8 IEVSNLVAHY--GSRQIL---HDVSLNVARGEIMVIMGGSGSGKTTLLSHLLGLKKPS-- 60 Query: 106 IISGKVIFNGMDIFSMTIDEFRKLLWKD-ISYVPQASQNAL----NPVLPISEIFYHEAI 160 +G V G DI ++ ++L + +++ A +++ N LP+ E Sbjct: 61 --AGTVRILGHDIARLSPIALQRLRTRTGVAFQSGALFSSMTVGDNIALPLRE------- 111 Query: 161 SHGEADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMD 220 H E D+ + L++V L LK P +LSGGM +R +A +++++P+L+ D Sbjct: 112 -HTELDETTIGIMTRLKLEVVSLAGFEHLK--PAELSGGMIKRAALARAIVMDPELLFCD 168 Query: 221 EPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVM 275 EP++ LD + + LI + MG++IV VTHD+ + +IA+R+ V+ KG+V+ Sbjct: 169 EPSAGLDPVVASSIDDLILRLRDAMGMSIVVVTHDLDSTFKIADRICVLDKGHVL 223 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: 188 Number of extensions: 10 Number of successful extensions: 2 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: 275 Length adjustment: 27 Effective length of query: 335 Effective length of database: 248 Effective search space: 83080 Effective search space used: 83080 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