Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate AZOBR_RS23030 AZOBR_RS23030 ABC transporter ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__azobra:AZOBR_RS23030 Length = 554 Score = 174 bits (440), Expect = 6e-48 Identities = 100/243 (41%), Positives = 156/243 (64%), Gaps = 12/243 (4%) Query: 23 RKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRK 82 RK A D+SL+++QG+ + ++GESG+GK+TLGR IVGL KP SG ++++G ++ R Sbjct: 298 RKVVAGDDLSLTIHQGETVGLVGESGSGKSTLGRSIVGLIKPDSGRILFEGVDLLSLSRP 357 Query: 83 IFKKYRKDVQLIPQDPYSTLPFNKTVEEILV-APILRWEKINKD-ELRKRLINLLELVKL 140 F+ YR+ VQ++ Q PY++L TV +I+ P+ E +K E K L+ L+ L Sbjct: 358 AFRPYRRHVQMVFQAPYASLNPRHTVGDIITQGPVAFGEDRHKALEKAKALLKLVGL-DA 416 Query: 141 TPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIK 200 + AE F PH+ SGGQ+QR+SIAR+L++ P++++ADEPV+ +D S++ +L+ L +++ Sbjct: 417 SAAERF----PHEFSGGQRQRISIARALALEPKLLIADEPVSALDVSVQAQVLDLLEDLR 472 Query: 201 NRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIK 260 +RLNL+M+FITHD+ IA VM GRIVE +E+ +P H YT L+ Sbjct: 473 HRLNLSMLFITHDLRIAAQIC-----DTIAVMQKGRIVEIGPAKEVFGNPQHAYTRTLLD 527 Query: 261 LTP 263 P Sbjct: 528 AIP 530 Score = 130 bits (327), Expect = 8e-35 Identities = 80/247 (32%), Positives = 137/247 (55%), Gaps = 14/247 (5%) Query: 26 YALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKP----TSGEVVYDGYNIWKNKR 81 +A++D++ ++ G++L V+GESG+GK+ ++GL +SGE+ + G N++ Sbjct: 24 HAVQDLTFTLEHGEILCVVGESGSGKSMTAHAVMGLLPKAVTVSSGEIRHQGTNVFSLPE 83 Query: 82 KIFKKYRKD-VQLIPQDPYSTL-PFNKTVEEILVAPILRWEK-INKDELRKRLINLLELV 138 + + R + +I Q+P + L P + ++I +LR+ +++ R R++ LL V Sbjct: 84 RDQRALRGGRIAMIFQEPMTALNPLMRVGDQI--DEVLRYHTTLDRAARRARVVELLASV 141 Query: 139 KLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAE 198 L + YP +LSGGQ+QR+ IA +L+V P I++ADEP T +D + + IL + + Sbjct: 142 GLPEPDHLRRSYPFRLSGGQRQRVMIAMALAVEPDILIADEPTTALDVTTQKQILELIQD 201 Query: 199 IKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDL 258 I+ + + ++FITHD + H VM G+IVE EE+L P HPYT L Sbjct: 202 IQAKRRMGVMFITHDFGVVAEIAH-----RVAVMQRGQIVEIGTAEEVLNRPKHPYTRQL 256 Query: 259 IKLTPSI 265 I P + Sbjct: 257 IAAVPHL 263 Lambda K H 0.321 0.141 0.410 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: 461 Number of extensions: 18 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: 324 Length of database: 554 Length adjustment: 32 Effective length of query: 292 Effective length of database: 522 Effective search space: 152424 Effective search space used: 152424 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: 50 (23.9 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