Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Dsui_2799 Dsui_2799 oligopeptide/dipeptide ABC transporter, ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__PS:Dsui_2799 Length = 670 Score = 181 bits (458), Expect = 7e-50 Identities = 114/315 (36%), Positives = 168/315 (53%), Gaps = 5/315 (1%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +L V NL + G R++ AV+ VSF V GE ++GESG GK+ A+LR + G Sbjct: 4 LLSVRNLKAGFLAGG-RVLTAVDGVSFAVAPGETFALLGESGCGKSATALALLRLLPNAG 62 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164 +I G+V G +I ++ R + + Q +LNPVL I H Sbjct: 63 RIQGGEVWLEGEEILALPEAAMRDRRGSAAAMIFQEPATSLNPVLTIGRQIGESLERHRG 122 Query: 165 ADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPT 223 + A LL VG+ DP R L+ YPFQLSGGMKQR MIA++L P+L++ DEPT Sbjct: 123 MKGEAARREALALLTAVGIADPERRLEEYPFQLSGGMKQRAMIAIALAGEPRLLIADEPT 182 Query: 224 SALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283 +ALD+ Q +L L+ + E + ++ +THD+ +A+ A+R+ VMY G ++E +E Sbjct: 183 TALDVTIQAQILDLLARLQAERAMGMLLITHDLGVVARSAHRVGVMYAGEIVETAPRQEF 242 Query: 284 IKSPLNPYTSLLVSSIPSL-KGEVKVINVPLDEP-LVSKEKGCPFLARCSKAFGRCKEEL 341 SP +PYT L +++P L + ++ +P P L + GC F RC A RC+ E Sbjct: 243 FASPRHPYTQKLFAALPDLGQRGAQLATIPGQVPGLAAMPAGCRFAPRCPVAMDRCRLES 302 Query: 342 PE-IRLVYDRKVRCH 355 P L +VRCH Sbjct: 303 PGWTELEAGHQVRCH 317 Score = 171 bits (433), Expect = 5e-47 Identities = 104/301 (34%), Positives = 176/301 (58%), Gaps = 14/301 (4%) Query: 63 IKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMDIFSMT 122 +KAV+ VS +++G L ++GESG GKTT A+LR + +G V +G ++ + Sbjct: 375 VKAVDGVSLELQRGRTLALVGESGCGKTTAGKAVLRLLPA-----TGSVRLDGRELLGLP 429 Query: 123 IDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEADKKRVIERAS--ELLKL 180 E + L + + V Q +LNP L + EI E ++ R RA+ LL+ Sbjct: 430 ERELKPLR-RRMQMVFQDPFASLNPRLTVGEII-EEGMTALRVAASRDERRAALAALLES 487 Query: 181 VGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLIKN 240 VGL PA L YP + SGG +QR+ IA +L + P+L++ DEPTSALD+ Q +L L++ Sbjct: 488 VGL-PAEALGRYPHEFSGGQRQRIAIARALAVQPELLVCDEPTSALDVSVQAQILNLLRR 546 Query: 241 INQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVSSIP 300 + +E+G+ +++TH+ + +A+ + VMY G ++E+G ++++ +P +PYT L+S++P Sbjct: 547 LQEELGLAYLFITHNFAVVEYLAHDVAVMYLGRIVEQGPVQQVLAAPCHPYTRALLSAVP 606 Query: 301 S--LKGEVKVINVPLDEPLVSK-EKGCPFLARCSKAFGRCKEELP-EIRLVYDRKVRCHL 356 L G+ +++ +P + P ++ +GC F RC++A RC++E P VRCHL Sbjct: 607 EPRLAGQREMVRLPGETPSPARPPQGCHFHPRCAQASERCRQEYPAPSTQAGGVVVRCHL 666 Query: 357 Y 357 Y Sbjct: 667 Y 667 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: 501 Number of extensions: 22 Number of successful extensions: 6 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: 670 Length adjustment: 34 Effective length of query: 328 Effective length of database: 636 Effective search space: 208608 Effective search space used: 208608 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: 52 (24.6 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