Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_094506802.1 CEV31_RS09385 ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >NCBI__GCF_002252445.1:WP_094506802.1 Length = 610 Score = 179 bits (453), Expect = 2e-49 Identities = 106/290 (36%), Positives = 170/290 (58%), Gaps = 12/290 (4%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +L + NL+V + G++R+ V+D+SF V G L ++GESGSGK+ +I+R G Sbjct: 9 LLNIENLSVEF--GSNRV---VDDLSFSVSPGRTLAVVGESGSGKSITSLSIMRLADVSG 63 Query: 105 -KIISGKVIFNG----MDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEA 159 K +G+++FNG D+ R + KDI+ + Q +LNPV I Sbjct: 64 AKFPTGRILFNGPDGERDLLKADQKTMRGIRGKDIAMIFQEPMTSLNPVFTIGNQLSEVL 123 Query: 160 ISHGEADKKRVIERASELLKLVGLDPAR-VLKMYPFQLSGGMKQRVMIALSLLLNPKLIL 218 + H K + LL++V L A +LK YP QLSGGM+QRVMIA++L PKL++ Sbjct: 124 MLHEGLSKTASLAEGKRLLEMVRLPDAEGLLKRYPHQLSGGMRQRVMIAMALACRPKLLI 183 Query: 219 MDEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEG 278 DEPT+ALD+ Q +L +IK++ +E+ + ++++THD+ +A++A+ ++VM+KG +EEG Sbjct: 184 ADEPTTALDVTIQAQILHIIKDLQKELEMAVIFITHDMGVVAEMADDVVVMWKGKKVEEG 243 Query: 279 KTEEIIKSPLNPYTSLLVSSIPSLKGEVKVINVPLDEPLVSKEKGCPFLA 328 I ++P +PYT L+SS+P L G + P P++ G P L+ Sbjct: 244 PVGRIFEAPQHPYTQTLLSSVPKL-GSMTGEAFPKRMPVMMMRDGVPVLS 292 Score = 144 bits (364), Expect = 5e-39 Identities = 81/242 (33%), Positives = 140/242 (57%), Gaps = 7/242 (2%) Query: 60 SRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMDIF 119 + + AV+ V+F + GE L ++GESGSGK+T+ I + P +SG + FNG Sbjct: 329 THVCNAVSKVAFDIYPGETLALVGESGSGKSTIGRTIQQLQSP----LSGDIRFNGKAYS 384 Query: 120 SMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEADKKRVIE-RASELL 178 M+ E K+ +++ Y+ Q +L+P + +HG D + I R +ELL Sbjct: 385 QMSSSERYKMR-REVQYIFQDPFASLDPRKTVGFSIAEPIRTHGLLDNNKAINARVAELL 443 Query: 179 KLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLI 238 + VGL P + YP + SGG +QR+ IA +L PKLI+ DE SALD+ Q ++ L Sbjct: 444 ERVGLGPEHASR-YPHEFSGGQRQRICIARALASKPKLIIADEALSALDVSIQAQVINLF 502 Query: 239 KNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVSS 298 ++ +E G+ ++++HD+ + ++++R+ V+Y G +ME G ++ ++P +PYT L+S+ Sbjct: 503 MDLQKEQGLAYLFISHDMAVVEKMSHRVAVLYLGQIMELGSRRQVFETPSHPYTQRLLSA 562 Query: 299 IP 300 +P Sbjct: 563 VP 564 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: 471 Number of extensions: 23 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 362 Length of database: 610 Length adjustment: 33 Effective length of query: 329 Effective length of database: 577 Effective search space: 189833 Effective search space used: 189833 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: 51 (24.3 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