Align CBP protein aka CebF, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate WP_106713054.1 CU102_RS21025 sugar ABC transporter permease
Query= TCDB::Q9X9R6 (306 letters) >NCBI__GCF_003010955.1:WP_106713054.1 Length = 342 Score = 124 bits (310), Expect = 4e-33 Identities = 95/315 (30%), Positives = 144/315 (45%), Gaps = 32/315 (10%) Query: 12 RWDMKASPYAFVAPFFLL-----FGAFSLVPLLYTAWYSLHNVQLSALDHKTWAGLDNYE 66 RW + + +A FFLL FG F L+P YS+ L + + G D Y Sbjct: 33 RWLQRTAGLGGMATFFLLPNMLIFGIFVLLPFFINFAYSMTGGAALFLPDRNFVGADQYA 92 Query: 67 NLL-----------SSDFFWNALKNTLTIGIISTVPQLLAALALAHLLNYKLRGSTAWRV 115 L + D FW A+ NT ++ + +L A +LN LR + WR Sbjct: 93 RLFDCSNYLDPNSCAEDTFWTAVGNTGWFVLLQVTLMIGVSLVTALILNRDLRARSFWRA 152 Query: 116 VMLTPYATSVAAATLVFTLLYSW---DGGMVNWILDFFGVDPVNW-RESDWGSQFAVSSI 171 V P V + +V L++ W G++N+ L G +P W + +W AV + Sbjct: 153 VFFFP----VLLSPVVVGLIWKWILQRQGLLNFGLYGLGFEPHAWLNDRNWSFAAAVG-V 207 Query: 172 VIWRWTGYNALIYLAAMQAIPADLYESAALDGANRWQQFRHVTVPQLRPTILFTVVVSTI 231 IW G+ LI LA +QAIP DLYE+A +DG + F +T+P L P +L +V+ I Sbjct: 208 SIWAHMGFYTLILLAGLQAIPKDLYEAAEMDGTKPTRVFLRITLPLLAPNLLVVIVLVLI 267 Query: 232 GATQLFGEPLLFGGVSGSKGGSEHQYQTLGLYMYDQGWI--IGNLGKASAIAWSMFLILL 289 A Q+F E + G GG L Y+Y+ G+ + N G A+A + M +L+ Sbjct: 268 RAVQIFDEVYVLTG-----GGPGTSTLFLTQYIYETGFAAQLRNPGLAAAASILMGAVLV 322 Query: 290 IVAAVNLLLTRRLRK 304 ++ + L L R K Sbjct: 323 VLTLLQLSLGRSSEK 337 Lambda K H 0.324 0.137 0.441 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: 310 Number of extensions: 21 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: 306 Length of database: 342 Length adjustment: 28 Effective length of query: 278 Effective length of database: 314 Effective search space: 87292 Effective search space used: 87292 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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