Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 208073 DVU2576 oligopeptide ABC transporter, ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >MicrobesOnline__882:208073 Length = 321 Score = 182 bits (462), Expect = 1e-50 Identities = 114/320 (35%), Positives = 176/320 (55%), Gaps = 11/320 (3%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +LEV L+V++D + I AV DVSF + G L I+GESG GK+ A+L + PG Sbjct: 5 LLEVQGLDVVFDI-EAGAIHAVRDVSFTLPHGRTLCIVGESGCGKSMTALALLGLVPAPG 63 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164 ++ + ++ F+G D+ ++ + R L ++ V Q +LNPV + + H Sbjct: 64 RVTARRLQFDGHDLTALDENGLRALRGHHMAMVFQDPMTSLNPVFRVGDQVAEALRLHLR 123 Query: 165 ADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPT 223 + E EL + VG+ P YP QLSGGM+QRVMIA++L P+L++ DEPT Sbjct: 124 LKGRAAREATIELFRQVGIPSPETRYDDYPHQLSGGMRQRVMIAMALSCGPRLLIADEPT 183 Query: 224 SALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283 +ALD+ Q +L L+ +I +++ +THD+ +A+ A+ ++VMY G ++E +E+ Sbjct: 184 TALDVTIQGQILGLLSDIAATGRASVLLITHDLGVVAETADDVIVMYAGAIVEHAPVQEL 243 Query: 284 IKSPLNPYTSLLVSSIPSLKGE----VKVI--NVPLDEPLVSKEKGCPFLARCSKAFGRC 337 SPL+PYT L+ S P + GE ++ I NVP PL GC F RC AF RC Sbjct: 244 FASPLHPYTRGLMRSAPPVHGERSPRLEAIRGNVP---PLDDLPSGCAFRDRCEHAFERC 300 Query: 338 KEELPEIRLVYDRKVRCHLY 357 P + + + VRC L+ Sbjct: 301 ATAAPPLFTLGKQMVRCWLH 320 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: 254 Number of extensions: 9 Number of successful extensions: 3 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: 321 Length adjustment: 28 Effective length of query: 334 Effective length of database: 293 Effective search space: 97862 Effective search space used: 97862 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