Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_011386731.1 AMB_RS22185 ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >NCBI__GCF_000009985.1:WP_011386731.1 Length = 533 Score = 144 bits (363), Expect = 5e-39 Identities = 88/241 (36%), Positives = 143/241 (59%), Gaps = 16/241 (6%) Query: 63 IKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMDIFSMT 122 +KAV+ +S +++G +G++GESGSGKTTL A+LR + G+I F G I SM+ Sbjct: 297 VKAVDGISLDLKRGHTIGVVGESGSGKTTLGLALLRLLDSDGEIS-----FGGTRIESMS 351 Query: 123 IDEFRKLLWKDISYVPQASQNALNPVLPISEIF-----YHEAISHGEADKKRVIERASEL 177 R L + + V Q +L+P + + +I HE H A++ R+I A Sbjct: 352 AGTLRPLR-RQMQMVFQDPYGSLSPRMSVGQIVGEGLEVHEPAMHA-AERDRLIAAA--- 406 Query: 178 LKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKL 237 L+ VGLDPA YP + SGG +QR+ IA +L+L PK I++DEPTSALD+ Q ++ L Sbjct: 407 LEEVGLDPA-TRDRYPHEFSGGQRQRIAIARALVLKPKFIVLDEPTSALDVSVQAQIVDL 465 Query: 238 IKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVS 297 ++++ + ++++HD+ + +A+ LLVM G V+E G+ +E+ K+P YT L++ Sbjct: 466 LRDLQARHALAYLFISHDLRVVRALADDLLVMKDGKVVEAGRADELFKAPRTAYTRALMA 525 Query: 298 S 298 + Sbjct: 526 A 526 Score = 139 bits (351), Expect = 1e-37 Identities = 82/243 (33%), Positives = 137/243 (56%), Gaps = 2/243 (0%) Query: 63 IKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIR-PPGKIISGKVIFNGMDIFSM 121 ++AV VSF + KGE L ++GESGSGK+ +IL+ + P G + +G ++ Sbjct: 20 VQAVKGVSFTLAKGETLALVGESGSGKSVTALSILQLLPYPRATHPRGSIRLDGAELVGA 79 Query: 122 TIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEADKKRVIERASELLKLV 181 RK+ I+ V Q +LNP+ I H + +R ELL LV Sbjct: 80 PEPALRKVRGGRIAMVFQEPMTSLNPLHSIEAQVGEVLELHLGLRGSTLRDRVVELLSLV 139 Query: 182 GL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLIKN 240 G+ +P + L P +LSGG +QRVMIA++L P +++ DEPT+ALD+ Q +L L+K Sbjct: 140 GIPEPEKRLGALPHELSGGQRQRVMIAMALAGEPDILIADEPTTALDVTIQAQILALLKG 199 Query: 241 INQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVSSIP 300 + +G+ ++++THD+ + ++A+R+ VM G ++E G ++ +P +PYT L+++ P Sbjct: 200 LQARLGMALLFITHDLGIVRKMADRVCVMNAGEIVESGPLPQVFDAPAHPYTQRLLAAEP 259 Query: 301 SLK 303 K Sbjct: 260 KGK 262 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: 393 Number of extensions: 17 Number of successful extensions: 3 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: 533 Length adjustment: 32 Effective length of query: 330 Effective length of database: 501 Effective search space: 165330 Effective search space used: 165330 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 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