Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 7025499 Shewana3_2653 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__ANA3:7025499 Length = 335 Score = 160 bits (405), Expect = 5e-44 Identities = 100/321 (31%), Positives = 175/321 (54%), Gaps = 12/321 (3%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +L+V NL + D + R+ +A+ VS + GEI G++GESGSG++ L AIL P Sbjct: 3 LLDVRNLTIELDTPHGRV-RALEKVSLTLNAGEIHGLVGESGSGRSLLARAILGIPGPNW 61 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164 I + +++++G ++ +MT E R L+ D++ + Q +L+P + + + Sbjct: 62 TITADRMMWDGNNLMAMTSKERRNLMGSDMAMIFQDPSGSLDPSQTVGSQLMQAMPKNPK 121 Query: 165 A----DKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILM 219 A K A + L VG+ +P +V+ Y ++LS G Q+VMIA+++ P+L++ Sbjct: 122 AYFWQKHKHAKLTAQKWLHKVGIKNPQKVMLSYAWELSEGECQKVMIAMAIANQPRLLIA 181 Query: 220 DEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGK 279 DEPT+++++ Q + +L+ +NQ V+I+ ++H++ +AQ + L V+Y G VME G Sbjct: 182 DEPTNSMELSTQAQIFRLLSQLNQLQNVSILIISHELETLAQWCDHLSVLYCGQVMESGP 241 Query: 280 TEEIIKSPLNPYTSLLVSSIPSLKG----EVKVINVPLDEP-LVSKEKGCPFLARCSKAF 334 TEE+I P +PYT L+ ++P G + + +P P L GC RC +A Sbjct: 242 TEELINQPYHPYTKALLDNMPDYSGIEAHKAIMPTLPGSAPALQHLPIGCRLGPRCPEAQ 301 Query: 335 GRCKEELPEIRLVYDRKVRCH 355 +C + P + + DR CH Sbjct: 302 KKCVNQ-PSLSHLRDRYFACH 321 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: 274 Number of extensions: 15 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: 335 Length adjustment: 29 Effective length of query: 333 Effective length of database: 306 Effective search space: 101898 Effective search space used: 101898 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 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