Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate Echvi_2704 Echvi_2704 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Cola:Echvi_2704 Length = 228 Score = 57.4 bits (137), Expect = 3e-13 Identities = 60/198 (30%), Positives = 101/198 (51%), Gaps = 27/198 (13%) Query: 40 VVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEIT 99 ++G SG GKTTL ++I L+ +G I + GE E+S + ++ R F G+ I Sbjct: 52 ILGPSGVGKTTLLHLI----AGFLSPQEGSIRI---GER-EVSQLKPSQMDR-FRGRHIG 102 Query: 100 IIPQA----AMNALMPTIRMEKYVRHLAESHGIDEEELLDKARRRFEEVGLDPLWIKRYP 155 ++ Q LM +++ +Y+ + S + ++GL + R P Sbjct: 103 MVFQQHHFIRSLDLMGNLQLIQYLAGKSPSP--------QAIKALLGQLGLGE-HLTRNP 153 Query: 156 FELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGIV--KSII 213 + +S G +QRA IA+A I PSL++ADEPTS+LD N ++K+L K Q + +I Sbjct: 154 YAMSQGEQQRAAIAMALINKPSLILADEPTSSLDDENCHAVVKLL---KDQALAHQADLI 210 Query: 214 FITHDIATVRQIADRMII 231 ITHD +I++ + + Sbjct: 211 IITHDQRLKGEISEAITL 228 Lambda K H 0.321 0.138 0.405 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: 128 Number of extensions: 6 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 330 Length of database: 228 Length adjustment: 25 Effective length of query: 305 Effective length of database: 203 Effective search space: 61915 Effective search space used: 61915 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: 47 (22.7 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