Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Ga0059261_3874 Ga0059261_3874 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Korea:Ga0059261_3874 Length = 243 Score = 90.5 bits (223), Expect = 4e-23 Identities = 69/215 (32%), Positives = 109/215 (50%), Gaps = 14/215 (6%) Query: 69 VSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMDIFSMTIDEFRK 128 VS V GE+ ++G SG GK+TL+ AIL + P + G+V G I M Sbjct: 31 VSVSVMPGELTLVVGPSGCGKSTLL-AILSGLTLPDQ---GEVDALGNPICRMKAGARDA 86 Query: 129 LLWKDISYVPQASQ--NALNPVLPISEIFYHEAISHGEADKKRVIERASELLKLVGLDPA 186 + +V Q NAL ++ + + EA +RA L+ VGL P Sbjct: 87 FRLANTGFVFQGFNLFNALTAEEQVAYVLQCMKVKPAEAR-----QRARAALEAVGLGPR 141 Query: 187 RVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLIKNINQEMG 246 +++ PF+LSGG KQRV IA +L P+++ DEPTSALD N ++ L+++I G Sbjct: 142 --MRLRPFELSGGEKQRVAIARALAKQPRILFADEPTSALDSHNGHAVIALLRDIAHNQG 199 Query: 247 VTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTE 281 ++ VTHD + A+R++ M G ++ + + + Sbjct: 200 AAVLCVTHD-PRLLSFADRIIHMEDGRIIRDERPD 233 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: 168 Number of extensions: 6 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: 243 Length adjustment: 26 Effective length of query: 336 Effective length of database: 217 Effective search space: 72912 Effective search space used: 72912 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