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 GFF92 Psest_0092 phosphonate C-P lyase system protein PhnK
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__psRCH2:GFF92 Length = 270 Score = 115 bits (287), Expect = 2e-30 Identities = 79/247 (31%), Positives = 127/247 (51%), Gaps = 12/247 (4%) Query: 23 KAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEFVEL- 81 K G+SF++ EV+G+VGESG GK+TL +++ V + G++++L Sbjct: 32 KGCQGVSFDLYPGEVLGIVGESGSGKSTLLSLLCGRCPPDRGSVQ---YRDAAGDWLDLY 88 Query: 82 --SSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHGIDEEELLDKARR 139 S R + R WG + Q + L + + + G+ L A Sbjct: 89 AASEAERRTLLRTEWG----FVEQNPRDGLRMGVSAGANIGERLMAQGVRHYGQLRAAGL 144 Query: 140 RF-EEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLLK 198 + ++V +DP I P SGGM+QR IA + +P L+ DEPT LDV Q LL Sbjct: 145 DWLQQVEIDPARIDDLPRTFSGGMQQRLQIARNLVSSPKLVFMDEPTGGLDVSVQARLLD 204 Query: 199 VLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQGL 258 +L + R+ + +++ +THD+A R +ADR+++M ++VE + +L+ P HPYTQ L Sbjct: 205 LLRGLVRE-LDLAVVIVTHDLAVARLLADRLMVMRRSRVVEAGLTDQILDDPQHPYTQLL 263 Query: 259 FNSVLTP 265 +SVL P Sbjct: 264 VSSVLQP 270 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: 198 Number of extensions: 13 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: 270 Length adjustment: 27 Effective length of query: 303 Effective length of database: 243 Effective search space: 73629 Effective search space used: 73629 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