Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate BWI76_RS26870 BWI76_RS26870 dipeptide ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Koxy:BWI76_RS26870 Length = 327 Score = 208 bits (530), Expect = 1e-58 Identities = 116/316 (36%), Positives = 195/316 (61%), Gaps = 7/316 (2%) Query: 45 ILEVHNLNVIY-DEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPP 103 +L V L+V + DEG +AV+ VS+ V +GE++GI+GESGSGK+ AI+ I P Sbjct: 3 LLNVDKLSVHFGDEGTP--FRAVDRVSYSVNQGEVVGIVGESGSGKSVSSLAIMGLIDYP 60 Query: 104 GKIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHG 163 G++++ K+ FNG D+ ++ E R+L+ +++ + Q +LNP + H Sbjct: 61 GRVMAEKLEFNGRDLKRISEKERRQLVGAEVAMIFQDPMTSLNPCYTVGYQIMEAIKVHQ 120 Query: 164 EADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEP 222 +KK I+RA +LL LVG+ DPA L +YP QLSGGM QRVMIA+++ PKL++ DEP Sbjct: 121 GGNKKTRIQRAIDLLTLVGIPDPASRLDVYPHQLSGGMSQRVMIAMAIACRPKLLIADEP 180 Query: 223 TSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEE 282 T+ALD+ Q +++L+ + Q+ + ++ +THD+ +A+ A++++VMY G V+E G ++ Sbjct: 181 TTALDVTIQAQIIELLLELQQKENMALILITHDLALVAEAAHKIIVMYAGQVVETGDAKD 240 Query: 283 IIKSPLNPYTSLLVSSIPSL-KGEVKVINVPLDEP-LVSKEKGCPFLARCSKAFGRCKEE 340 I ++P +PYT L+ ++P + + ++ ++P P + GC RC A +C+ E Sbjct: 241 IFRAPRHPYTQALLRALPEFAQDKARLASLPGVVPGKYDRPSGCLLNPRCPYATDKCRSE 300 Query: 341 LPEIRLVY-DRKVRCH 355 PE+ L+ R+ +CH Sbjct: 301 EPELNLLNGGRQSKCH 316 Lambda K H 0.319 0.138 0.391 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: 287 Number of extensions: 10 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: 362 Length of database: 327 Length adjustment: 29 Effective length of query: 333 Effective length of database: 298 Effective search space: 99234 Effective search space used: 99234 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