Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Ga0059261_2703 Ga0059261_2703 ABC-type multidrug transport system, ATPase component
Query= uniprot:D8IUD1 (522 letters) >FitnessBrowser__Korea:Ga0059261_2703 Length = 313 Score = 95.5 bits (236), Expect = 2e-24 Identities = 73/220 (33%), Positives = 115/220 (52%), Gaps = 12/220 (5%) Query: 12 PLLTLSGIGKRYAA--PVLDGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGM 69 P+L++ G+ K YA+ L +DLD+ G++ AL G NGAGK+TL IICG+V S+G + Sbjct: 3 PILSVRGVSKTYASGHKALGSVDLDINKGEIFALLGPNGAGKTTLISIICGIVTPSSGTI 62 Query: 70 MLDGQPYAPASRTQAEGLGIRMVMQELNLIPTLSIAENLFLEKLPRRFGWIDRKKLAEAA 129 ++DG + S +A + I +V QEL++ ++ + R FG + A A Sbjct: 63 VVDG--HDAISEPRAARMKIGLVPQELSVDMFETVQATTRYSR--RLFG-----RPANDA 113 Query: 130 RAQMEVVGLGELDPW-TPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELL 188 + L D + V +L G ++ V IA+ L L LDEPTA + + Sbjct: 114 YIDQVLKDLSLYDKRNSKVMELSGGMKRRVLIAKALAHEPDILFLDEPTAGVDVSLRRDM 173 Query: 189 FSRIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLV 228 + I LR G II +H +EE + +ADR+ V+ G+L+ Sbjct: 174 WKLIGSLRERGTTIILTTHYIEEAEEMADRVGVINKGELL 213 Score = 73.6 bits (179), Expect = 1e-17 Identities = 53/227 (23%), Positives = 108/227 (47%), Gaps = 24/227 (10%) Query: 264 PVLRIRGLGRA-----PVVHPASLALHAGEVLGIAGLIGSGRTELLRLIFGADRAEQGEI 318 P+L +RG+ + + L ++ GE+ + G G+G+T L+ +I G G I Sbjct: 3 PILSVRGVSKTYASGHKALGSVDLDINKGEIFALLGPNGAGKTTLISIICGIVTPSSGTI 62 Query: 319 FIGDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLANLGSVSRGG--ML 376 + + R+ + +K G L+PQ +SV+ + + +R + Sbjct: 63 VVDGHDAISEPRAAR--MKIG-------------LVPQELSVDM-FETVQATTRYSRRLF 106 Query: 377 DHAAESSVAQDYVKKLRIRSGSVAQAAGELSGGNQQKVVIARWLYRDCPIMLFDEPTRGI 436 A + +K L + ++ ELSGG +++V+IA+ L + I+ DEPT G+ Sbjct: 107 GRPANDAYIDQVLKDLSLYDKRNSKVM-ELSGGMKRRVLIAKALAHEPDILFLDEPTAGV 165 Query: 437 DIGAKSDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGRI 483 D+ + D+++L L +G +++ + + E ++ DR+ V++ G + Sbjct: 166 DVSLRRDMWKLIGSLRERGTTIILTTHYIEEAEEMADRVGVINKGEL 212 Lambda K H 0.320 0.137 0.390 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: 378 Number of extensions: 23 Number of successful extensions: 5 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: 522 Length of database: 313 Length adjustment: 31 Effective length of query: 491 Effective length of database: 282 Effective search space: 138462 Effective search space used: 138462 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