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 CCNA_02404 CCNA_02404 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Caulo:CCNA_02404 Length = 278 Score = 94.0 bits (232), Expect = 4e-24 Identities = 75/234 (32%), Positives = 118/234 (50%), Gaps = 13/234 (5%) Query: 26 DGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEFVELSSMT 85 DGL ++ + E++GVVG SG GK+ L N I + T DG + R+ G + ++S Sbjct: 37 DGLDLKVEQGEILGVVGGSGSGKSVLLNSI----IGLKTPDDGHV--RLFGGDMRVASRR 90 Query: 86 RDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHGIDEEELLDKARRRFEEVG 145 R + WG + Q A+ + + T+R E L E + E+ A + VG Sbjct: 91 RWSSVERRWG---VLFQQGALFSNL-TVR-ENVAAPLYEHTRLPRSEVEAIADLKIAMVG 145 Query: 146 LDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLLKVLMQMKR 205 L P ELSGGMR+RA +A A ++P LL DEPT+ LD + + L++ Sbjct: 146 LPARAATLKPAELSGGMRKRAGLARALAMDPELLFLDEPTAGLDPIGAQA-FDALIKDLS 204 Query: 206 QGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQGLF 259 + ++ ITHD+ ++ I DR+ ++ K+V APV LE+ HP+ + F Sbjct: 205 DSLELTVFMITHDLDSLYTITDRVAVLADKKVVTVAPVGE-LERSDHPWIKQYF 257 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: 201 Number of extensions: 14 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: 278 Length adjustment: 27 Effective length of query: 303 Effective length of database: 251 Effective search space: 76053 Effective search space used: 76053 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