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 HSERO_RS16725 HSERO_RS16725 ABC transporter permease
Query= TCDB::Q9X9R6 (306 letters) >FitnessBrowser__HerbieS:HSERO_RS16725 Length = 299 Score = 110 bits (276), Expect = 3e-29 Identities = 78/270 (28%), Positives = 126/270 (46%), Gaps = 9/270 (3%) Query: 22 FVAPFFLLFGAFSLVPLLYTAWYSLHNVQLSALDHKTWAGLDNYENLLSSDFFWNALKNT 81 F+AP +L F PL W + ++ ++ GLDN+ L +L NT Sbjct: 16 FMAPAVILLVVFLTYPLGLGIWLGFTDTKIGG--EGSFIGLDNFTYLAGDSLAQLSLFNT 73 Query: 82 LTIGIISTVPQLLAALALAHLLNYKLRGSTAWRVVMLTPYATSVAAATLVFTLLYSWDGG 141 + + +++ + + L LA LLN + T +R ++L P+ A + L F LY Sbjct: 74 VFYTVSASILKFMLGLWLAILLNKNVPLKTFFRAIVLLPWIVPTALSALAFWWLYDAQFS 133 Query: 142 MVNWILDFFGVDP--VNWRESDWGSQFAVSSIVIWRWTGYNALIYLAAMQAIPADLYESA 199 +++W L G+ +++ W ++++ +WR + A+ LA +Q I LYE+A Sbjct: 134 VISWALHKMGLIDRYIDFLGDPWNARWSTVFANVWRGIPFVAISLLAGLQTISPSLYEAA 193 Query: 200 ALDGANRWQQFRHVTVPQLRPTILFTVVVSTIGATQLFGEPLLFGGVSGSKGGSEHQYQT 259 A+DGA WQQFRHVT+P L P I + S + F L++ G + H T Sbjct: 194 AIDGATPWQQFRHVTLPLLTPIIAVVMTFSVLFTFTDF--QLIYVLTRGGPLNATHLMAT 251 Query: 260 LGLYMYDQGWIIGNLGKASAIAWSMFLILL 289 L G G LG+ +A+A M LL Sbjct: 252 LSFQRAIPG---GALGEGAALATYMIPFLL 278 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: 302 Number of extensions: 24 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: 306 Length of database: 299 Length adjustment: 27 Effective length of query: 279 Effective length of database: 272 Effective search space: 75888 Effective search space used: 75888 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 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