Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate BWI76_RS17225 BWI76_RS17225 oligopeptide ABC transporter ATP-binding protein OppD
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Koxy:BWI76_RS17225 Length = 337 Score = 192 bits (489), Expect = 8e-54 Identities = 109/302 (36%), Positives = 172/302 (56%), Gaps = 5/302 (1%) Query: 44 MILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPP 103 ++L+V +L V + + + AVND++F + GE LGI+GESGSGK+ A++ + Sbjct: 18 LLLDVKDLRVTFGTPDGDVT-AVNDLNFNLRAGETLGIVGESGSGKSQTAFALMGLLAAN 76 Query: 104 GKIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHG 163 G+I G FNG I ++ E KL + IS + Q +LNP + + E + H Sbjct: 77 GRI-GGSATFNGKQILNLPERELNKLRAEQISMIFQDPMTSLNPYMRVGEQLMEVLMLHK 135 Query: 164 EADKKRVIERASELLKLVGLDPARV-LKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEP 222 K E + ++L V + AR +KMYP + SGGM+QRVMIA++LL PKL++ DEP Sbjct: 136 ALSKAEAFEESVKMLDAVKMPEARKRMKMYPHEFSGGMRQRVMIAMALLCRPKLLIADEP 195 Query: 223 TSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEE 282 T+ALD+ Q ++ L+ + +E I+ +THD+ +A I +++LVMY G ME G+ + Sbjct: 196 TTALDVTVQAQIMTLLNELKREFNTAIIMITHDLGVVAGICDKVLVMYAGRTMEYGQARD 255 Query: 283 IIKSPLNPYTSLLVSSIPSLKGE-VKVINVPLDEP-LVSKEKGCPFLARCSKAFGRCKEE 340 + P +PY+ L++++P L E ++ +P + P L+ KGCPF RC A C Sbjct: 256 VFYQPSHPYSIGLLNAVPRLDAEGDALLTIPGNPPNLLRLPKGCPFQPRCPHAMEICNSA 315 Query: 341 LP 342 P Sbjct: 316 PP 317 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: 262 Number of extensions: 12 Number of successful extensions: 4 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: 337 Length adjustment: 29 Effective length of query: 333 Effective length of database: 308 Effective search space: 102564 Effective search space used: 102564 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