Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_048081181.1 EJ01_RS06730 ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >NCBI__GCF_000745485.1:WP_048081181.1 Length = 566 Score = 128 bits (321), Expect = 4e-34 Identities = 91/253 (35%), Positives = 146/253 (57%), Gaps = 13/253 (5%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +++V NL+ Y N IKA+ND++ VE+GEI+GIIG SGSGKT+L+ ILR + P Sbjct: 1 MIKVENLSKTYKIENGGEIKALNDINLNVEEGEIVGIIGMSGSGKTSLLR-ILRGVEP-- 57 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQAS-----QNAL-NPVLPISEIFY-H 157 SGK+ +G+++ + + L K + Q S + AL N V ++ Y Sbjct: 58 -FDSGKITLDGIEVSPDSSPYYFAKLKKATAIHLQRSFGLWGETALQNVVRKLAGAKYGD 116 Query: 158 EAISHGEADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLI 217 E++ + ++A E+L++VGL + + LSGG KQR+++A L PK++ Sbjct: 117 ESLQDVDDAVAEFGDQAKEILEIVGL--GHKINHFAPVLSGGEKQRLIMARQLAKKPKVL 174 Query: 218 LMDEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEE 277 L+DEP + ++ +L IKNIN+E+GVTIV V+H +++RL++M G +++E Sbjct: 175 LLDEPATMSCPRTKQEILDAIKNINKELGVTIVLVSHLPEVHRYLSDRLVLMENGEIIDE 234 Query: 278 GKTEEIIKSPLNP 290 G TEEII + P Sbjct: 235 GSTEEIITKFMEP 247 Score = 80.5 bits (197), Expect = 1e-19 Identities = 73/292 (25%), Positives = 136/292 (46%), Gaps = 57/292 (19%) Query: 45 ILEVHNLN---VIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIR 101 I++V++L+ + GN+ IK DV+F ++KGEI+ +IG SG+GKT L+ I Sbjct: 264 IIKVNDLDKRFFLLKGGNTLQIK---DVNFDIKKGEIVSLIGPSGAGKTVLLRMIAGLDA 320 Query: 102 PPGKIISGKVIFNGMDIFSMTIDEF---RKLLW-----------------------KDIS 135 P I K+ N +D+ + ++ RKL + KD Sbjct: 321 PDSGSILFKLDDNWVDMQDLGLERMNVRRKLGFMHQEFALTHYATIKDQIAARLGVKDEH 380 Query: 136 YVPQASQNA---------LNPVLPISEIFYHEAISHGEADKKR---------------VI 171 + +A + A L+ + ++++ HEA + E + + V Sbjct: 381 VISKARKTAEELGISDKILDVLYQLTDLPEHEAKARLEKIELKPDILDLLFPKFPDTEVR 440 Query: 172 ERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQ 231 + A + K + L P +L ++LSGG K R +AL L P ++++DEP LD + Sbjct: 441 KYAEPIFKALDL-PLDILDRCSYELSGGQKVRATLALVLTSKPDVLILDEPFGDLDPITL 499 Query: 232 ELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283 ++ +K IN+E TI+ V+H + I ++ R +++ G ++ +G +++ Sbjct: 500 RIVSNSLKRINKEFNTTILMVSHHVDFIREVTTRAIMIEDGKLVGDGDPQKL 551 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: 441 Number of extensions: 18 Number of successful extensions: 4 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: 566 Length adjustment: 33 Effective length of query: 329 Effective length of database: 533 Effective search space: 175357 Effective search space used: 175357 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