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 6937163 Sama_1333 lipoprotein releasing system ATP-binding protein LolD (RefSeq)
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__SB2B:6937163 Length = 229 Score = 97.4 bits (241), Expect = 3e-25 Identities = 73/237 (30%), Positives = 123/237 (51%), Gaps = 14/237 (5%) Query: 1 MKEILLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMV 60 M++ILLK ENV Y+ K+ + + G+ + E + +VG SG GK+TL +++ ++ Sbjct: 1 MQDILLKVENVSKTYREGKLETQVLCGVDLSVYRGEQLAIVGGSGSGKSTLLHIMG-SLD 59 Query: 61 KPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVR 120 KP + GK+ L + LS+ + +++ G I Q + L+P + V Sbjct: 60 KPTS---GKVLLE-GEDLYSLSAARQAQIRNASLG----FIYQ--FHHLLPEFSALENVA 109 Query: 121 HLAESHGIDEEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLI 180 A G+D++ +A E VGL + P ELSGG RQR IA A I P L++ Sbjct: 110 MPARIAGVDKKTAFGRAEALLERVGLSHR-LSHAPSELSGGERQRVAIARALINQPRLVL 168 Query: 181 ADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKI 237 ADEPT LD + + + ++ ++ Q + + + +THD A ++ DR + M +GK+ Sbjct: 169 ADEPTGNLDAASGEAVYALIRELAAQ-LGTAFVVVTHDNALAARM-DRQLSMKSGKL 223 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: 146 Number of extensions: 7 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: 330 Length of database: 229 Length adjustment: 25 Effective length of query: 305 Effective length of database: 204 Effective search space: 62220 Effective search space used: 62220 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