Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_052287789.1 MAEO_RS01500 ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >NCBI__GCF_000017185.1:WP_052287789.1 Length = 383 Score = 106 bits (264), Expect = 1e-27 Identities = 77/260 (29%), Positives = 132/260 (50%), Gaps = 28/260 (10%) Query: 52 NVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKV 111 NV GN I+ N+VS V GEI+ ++G SG GKTTL+ I ++ SG + Sbjct: 6 NVSKKMGNQNIL---NNVSLQVHDGEIMVLLGPSGCGKTTLLKIIAGLLKQD----SGNI 58 Query: 112 IFNGMDIFSMTIDEFRK-LLWKDISYVPQASQNALNPVLPISEIFYHEAISHG----EAD 166 I N I E +++D + P + ++ I+ G + Sbjct: 59 IINNNIINDFPSKERNMGFVFQDYALFPHKN--------------VYDNIAFGLKLRKVP 104 Query: 167 KKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSAL 226 + + + +E+++++ +D + K+ QLSGG KQRV +A +L+++P ++L+DEP SAL Sbjct: 105 ENEINIKINEIMEILEIDHLKDKKIP--QLSGGQKQRVALARALVIDPDVLLLDEPLSAL 162 Query: 227 DMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKS 286 D + +E L + +K I +GVT +YVTHD+ + + + VM G + + K ++I Sbjct: 163 DPILREKLREELKTILNTLGVTGIYVTHDLTEAMILGDNVAVMNNGIIQQIEKPDDIFYH 222 Query: 287 PLNPYTSLLVSSIPSLKGEV 306 P N + + V LKG + Sbjct: 223 PKNEFVAEFVGVKNILKGRI 242 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: 368 Number of extensions: 21 Number of successful extensions: 2 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: 383 Length adjustment: 30 Effective length of query: 332 Effective length of database: 353 Effective search space: 117196 Effective search space used: 117196 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 Apr 09 2024. 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