Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate SM_b20141 SM_b20141 oligopeptide ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Smeli:SM_b20141 Length = 548 Score = 193 bits (490), Expect = 1e-53 Identities = 103/258 (39%), Positives = 168/258 (65%), Gaps = 4/258 (1%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAI-RPP 103 +LEV NL+V + + ++ AV +S+ ++KGE L I+GESGSGK+ SAI+ I PP Sbjct: 5 LLEVRNLSVEFHTA-AGVVHAVKSISYHLDKGETLAILGESGSGKSVSSSAIMNLIDMPP 63 Query: 104 GKIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHG 163 G+I SG+++ +G D+ +M +E R++ + ++ + Q + LNPV + +HG Sbjct: 64 GRISSGEILLDGRDLLTMPAEERREVNGRRVAMIFQDPLSHLNPVYSVGWQISEAMTTHG 123 Query: 164 EADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEP 222 A K E A LL+ VG+ +P R ++ YP + SGG +QRVMIA++L L P L++ DEP Sbjct: 124 LAGSK-AREEALRLLRRVGIPEPERAMRKYPHEFSGGQRQRVMIAMALALRPDLLIADEP 182 Query: 223 TSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEE 282 T+ALD+ Q +LKL+K + +E G+ ++ +THD+ +++IA+R++VM KG ++E G E Sbjct: 183 TTALDVTVQAEVLKLLKELQRETGMAVLIITHDLGVVSEIADRVVVMEKGAIVEAGTVRE 242 Query: 283 IIKSPLNPYTSLLVSSIP 300 I K+P +PYT L+++ P Sbjct: 243 IYKNPQHPYTQKLIAAAP 260 Score = 146 bits (368), Expect = 1e-39 Identities = 83/236 (35%), Positives = 138/236 (58%), Gaps = 7/236 (2%) Query: 64 KAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMDIFSMTI 123 +A+ +SF + GE + ++GESGSGK+TL A+LR P SG ++ G D+F+++ Sbjct: 289 EALKGISFDLMPGETMAVVGESGSGKSTLARALLRLDEPD----SGTALWKGRDLFALSP 344 Query: 124 DEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEA-DKKRVIERASELLKLVG 182 E KL +D+ V Q +LNP + + ++ + H + K + ER +ELL VG Sbjct: 345 AELYKLR-RDLQMVFQDPTQSLNPRMTVYQLISEAWVIHPDILPKAKWRERVAELLVQVG 403 Query: 183 LDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLIKNIN 242 L A + YP Q SGG +QR+ IA +L L P+LI+ DE SALD+ Q +++L+ + Sbjct: 404 LS-AEHMSRYPHQFSGGQRQRIAIARALALEPQLIICDEAVSALDVSVQAQVIELLDRLR 462 Query: 243 QEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVSS 298 +EMG+ +++ HD+ + A+ ++VM +G V+E G E+ +P YT L+++ Sbjct: 463 REMGIAFIFIAHDLPVVRDFADYVMVMQQGEVVELGTVREVFDTPRQAYTRALLAA 518 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: 413 Number of extensions: 13 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: 548 Length adjustment: 32 Effective length of query: 330 Effective length of database: 516 Effective search space: 170280 Effective search space used: 170280 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