Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate GFF2860 HP15_2804 oligopeptide/dipeptide ABC transporter, ATP-binding protein-like protein
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Marino:GFF2860 Length = 672 Score = 187 bits (476), Expect = 5e-52 Identities = 113/307 (36%), Positives = 182/307 (59%), Gaps = 16/307 (5%) Query: 3 LMELKGVSVIFEDKVGLFKKRK-FYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGL 61 ++ + VS F + G+F KRK AL DVSL++ +G++L ++GESG GKTTL R I+GL Sbjct: 352 ILTVDHVSCTFSVRRGMFGKRKPLQALDDVSLTLKKGEVLALVGESGCGKTTLTRTIMGL 411 Query: 62 QKPTSGEVVYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEK 121 Q P++G V +G I +N + + + +Q I QDPYS+L KT+ EI+ P+ Sbjct: 412 QAPSTGSVTLNGQRI-ENLPPMDRA--RMIQPIFQDPYSSLNPRKTIGEIIAKPLFVHGI 468 Query: 122 INKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPV 181 + E +++ ++ELV L P+ F YP QLSGGQ+QR +I R+L +NP +++ DEP Sbjct: 469 GSNQEQHQQVRKMMELVGL-PSRVF-NSYPDQLSGGQRQRAAIGRALILNPEVVICDEPT 526 Query: 182 TMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERA 241 + +D S++ ILN L ++++ L+LT +F+TH++ + + H+ D+ VM+ G IVE Sbjct: 527 SALDVSVQAQILNLLLDLRDELDLTYLFVTHNLSVVQ---HMADR--VAVMYLGEIVECG 581 Query: 242 DLEEILKDPLHPYTNDLIKLTPSIDNLYKEINVKI-----NYERVEKGCPYRLRCPFAMD 296 + ++++ DP HPYT+ L+ SI + + N GCP+ RCP A Sbjct: 582 ERDQVMSDPKHPYTHALMNSALSISPGESVPDPGLSGDFPNPMNRPSGCPFHPRCPLADQ 641 Query: 297 ICKNEEP 303 C+ + P Sbjct: 642 QCREQAP 648 Score = 144 bits (363), Expect = 6e-39 Identities = 89/295 (30%), Positives = 155/295 (52%), Gaps = 28/295 (9%) Query: 26 YALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGE----VVYDGYNIWK-NK 80 +A++ +SL +N+G+ L ++GESG+GK+ ++ L P + + +DG ++ + Sbjct: 24 HAVRGISLELNRGETLGIVGESGSGKSMTALALMNLLPPAAKRQASCIDFDGSDLTHATE 83 Query: 81 RKIFKKYR-KDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVK 139 R++ K R + + +I Q+P ++L ++ L + K++ E R + LLE V Sbjct: 84 RELASKIRGQRIGMIFQEPMTSLNPVYSIGRQLKETMTLHRKVSDTEAENRAVYLLEKVG 143 Query: 140 LTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEI 199 L L +YPH+LSGGQ+QR+ IA +L P +++ADEP T +D +++ IL+ L E+ Sbjct: 144 LPDPASRLKQYPHELSGGQRQRVMIAMALMNEPELLIADEPTTALDVTIQAQILHLLREL 203 Query: 200 KNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLI 259 + ++M+ ITHD+ + N VM+AG IVE E+L++P HPYT L+ Sbjct: 204 QQEFGMSMILITHDLGVVSR-----AADNIAVMYAGDIVETGKTGEVLENPRHPYTKGLL 258 Query: 260 KLTP-----------SIDNLYKEINVKINYERVEKGCPYRLRCPFAMDICKNEEP 303 + P +I + + I+ GC + RCP A +C+ P Sbjct: 259 ECVPGYKGQSQQRLGAIPGIVPAMTGDIS------GCAFASRCPRAAGVCRTTNP 307 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: 566 Number of extensions: 24 Number of successful extensions: 9 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: 672 Length adjustment: 33 Effective length of query: 291 Effective length of database: 639 Effective search space: 185949 Effective search space used: 185949 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