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 203521 SO4446 molybdenum ABC transporter, ATP-binding protein (NCBI ptt file)
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__MR1:203521 Length = 367 Score = 72.8 bits (177), Expect = 1e-17 Identities = 69/222 (31%), Positives = 108/222 (48%), Gaps = 17/222 (7%) Query: 30 FEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVD-GKIFLRVNGEFVELSSMTRDE 88 F EV+ VVG SG GKTTL + M+ L D G I V GE + +R Sbjct: 24 FSCKAGEVLAVVGPSGGGKTTL-----LRMIAGLNHPDAGSI---VFGETPWFDNKSRTA 75 Query: 89 VKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHGIDEEELLDKARRRFEEVGLDP 148 + + + I +PQ L P + + V +A I + + +A+ + V L Sbjct: 76 LTPQ--QRHIGYMPQHF--GLFPNLTALENV--VAGLDHIPKSARIARAKDWLDRVNLQG 129 Query: 149 LWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGI 208 L R P LSGG RQR +A A PS+L+ DEP SA+D ++ L L ++K Q + Sbjct: 130 L-PDRLPMHLSGGQRQRVALARALAREPSVLLLDEPFSAVDRETRERLYLELARLKEQ-L 187 Query: 209 VKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKP 250 + +I +THD+ +AD MI++ G++++ +L +P Sbjct: 188 LCPVIMVTHDLNEALLLADSMILISQGQMLQQGVPFEVLSRP 229 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: 255 Number of extensions: 11 Number of successful extensions: 3 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: 367 Length adjustment: 29 Effective length of query: 301 Effective length of database: 338 Effective search space: 101738 Effective search space used: 101738 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: 49 (23.5 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