Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Ac3H11_4315 ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4315 Length = 568 Score = 181 bits (460), Expect = 3e-50 Identities = 100/259 (38%), Positives = 152/259 (58%), Gaps = 2/259 (0%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +LEV NL + Y E + + V+ VSF + GE++ ++GESGSGKTT +I+ + G Sbjct: 12 VLEVENLAIAYREKDHEQ-RVVHGVSFSIAPGEVVALVGESGSGKTTTAQSIIGLLADNG 70 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164 ++ G + NG DI + D F + + +S +PQ ++LNPV E H Sbjct: 71 RVEQGAIRLNGTDIAGWSADRFDTVRGRVVSLIPQDPTSSLNPVRTAGEQVGEILQIHRY 130 Query: 165 ADKKRVIERASELLKLVGLD-PARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPT 223 D++ + +R ELL VGL P + YP +LSGGMKQRV+IA+++ L P LI+ DEPT Sbjct: 131 GDRQAIAQRVVELLAKVGLSQPELRARQYPHELSGGMKQRVLIAIAIALQPALIIADEPT 190 Query: 224 SALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283 SALD+ Q +L LI + E G ++ VTHD+ A A+RL+V+ G + E+G T + Sbjct: 191 SALDVTVQRRILDLIDGLRAEFGTAVLLVTHDLGVAADRAHRLVVLQGGRIQEQGDTGSV 250 Query: 284 IKSPLNPYTSLLVSSIPSL 302 +++P + YT L++ PSL Sbjct: 251 LRNPQSAYTRKLLADAPSL 269 Score = 135 bits (341), Expect = 2e-36 Identities = 79/246 (32%), Positives = 140/246 (56%), Gaps = 6/246 (2%) Query: 58 GNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMD 117 G +AV+ VSF V +G I+GESGSGKTT I ++ +P +G ++ GMD Sbjct: 307 GRKEPFRAVDGVSFRVRRGTTHAIVGESGSGKTTTIRNVVGFRQPT----AGHIVIEGMD 362 Query: 118 IFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEADKKRVIERASEL 177 + ++ + R+ + + V Q ++L+P I +I ++ R ++ Sbjct: 363 LTTLRGEALRQFR-RTVQLVYQNPFSSLDPRQTIFQIIEEPLLNFDPLPAAERARRVHDI 421 Query: 178 LKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKL 237 L VGL P VL+ P LSGG +QRV IA +L+L P+++++DE SALD+ Q +L L Sbjct: 422 LARVGLPPT-VLERRPRALSGGQRQRVAIARALILQPRVLVLDEAVSALDVTVQAQILAL 480 Query: 238 IKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVS 297 ++ + +++G+T ++++HD+ + QIA+ + V+ G ++ G+ E++ P + YT L++ Sbjct: 481 LETLQRDLGLTYLFISHDLAVVRQIADTVSVLQGGRQVDAGRVEDVFLRPGSDYTRELIA 540 Query: 298 SIPSLK 303 +IP K Sbjct: 541 AIPGKK 546 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: 448 Number of extensions: 20 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: 568 Length adjustment: 33 Effective length of query: 329 Effective length of database: 535 Effective search space: 176015 Effective search space used: 176015 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