Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_035131541.1 Q763_RS04180 ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >NCBI__GCF_000769915.1:WP_035131541.1 Length = 562 Score = 175 bits (444), Expect = 2e-48 Identities = 95/249 (38%), Positives = 155/249 (62%), Gaps = 12/249 (4%) Query: 66 VNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG--KIISGKVIFNGMDIFSMTI 123 V+D +F +E+ EILGI+GESGSGK+ A++ + P G ++ G + F G DI +T Sbjct: 25 VHDSTFTLEQNEILGIVGESGSGKSVTSLAVM-GLLPKGILQVTQGSIAFEGRDISQLTT 83 Query: 124 DEFRKLLWKDISYVPQASQNALNPVLP----ISEIFYHEAISHGEADKKRVIERASELLK 179 E R + DI+ + Q ++LNP L + EIF H K+ + L + Sbjct: 84 REMRNIRGNDIAMIFQEPMSSLNPSLKCGYQVEEIFKE----HTSLSKREIKATVLSLFE 139 Query: 180 LVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLI 238 V L +P ++ YP ++SGG KQRVMIA+++ PK+++ DEPT+ALD+ Q+ ++ L+ Sbjct: 140 KVKLPNPEKIYNRYPHEISGGQKQRVMIAMAIACKPKILIADEPTTALDVTVQKEIILLL 199 Query: 239 KNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVSS 298 K + QE ++I++++HD+ +++IANR+LVMYKG ++E+G EI ++P + YT L++S Sbjct: 200 KELQQETKMSIIFISHDLSLVSEIANRVLVMYKGNIVEQGVATEIFENPKHTYTKALINS 259 Query: 299 IPSLKGEVK 307 PSL +K Sbjct: 260 RPSLDVRLK 268 Score = 148 bits (374), Expect = 3e-40 Identities = 91/263 (34%), Positives = 149/263 (56%), Gaps = 14/263 (5%) Query: 45 ILEVHNLNVIYDE-----GNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRA 99 +LEV N+ Y G KAVN+VSF + +GE LG++GESG GK+TL +AIL+ Sbjct: 304 LLEVINVEKEYVSSSGLFGRDVKFKAVNNVSFKIYEGETLGLVGESGCGKSTLGNAILQL 363 Query: 100 IRPPGKIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEA 159 K +G +++ G D+ ++ R+L K+I + Q ++LNP + + + Sbjct: 364 ----DKATAGSILYKGQDLTKLSASAIRELR-KEIQIIFQDPYSSLNPRITVGKAIMEPM 418 Query: 160 ISHG--EADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLI 217 HG + D++R E+ E+LK VGL YP + SGG +QRV IA ++ L PKLI Sbjct: 419 KVHGLYKNDRERR-EKTIEILKRVGLGEEH-FNRYPHEFSGGQRQRVGIARTIALQPKLI 476 Query: 218 LMDEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEE 277 + DE SALD+ Q +L L+ + + G T ++++HD+ + +++++LVM KG + E Sbjct: 477 VCDESVSALDISVQAQVLNLLNELKENFGFTYIFISHDLAVVKYMSDQVLVMNKGQIEEM 536 Query: 278 GKTEEIIKSPLNPYTSLLVSSIP 300 + + + + P YT L+ +IP Sbjct: 537 NEADALYEHPEKEYTKKLIEAIP 559 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: 22 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: 562 Length adjustment: 33 Effective length of query: 329 Effective length of database: 529 Effective search space: 174041 Effective search space used: 174041 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