Align deoxynucleoside transporter, ATPase component (characterized)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_607 Length = 517 Score = 306 bits (785), Expect = 9e-88 Identities = 189/518 (36%), Positives = 292/518 (56%), Gaps = 23/518 (4%) Query: 9 APLSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPD 68 AP + P L++ G+HK+F G+ LR V L+ G+I+ L+G+NG GKSTLIK+++G Sbjct: 12 APAAAPVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEAS 71 Query: 69 EGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTF 128 GQ+ + G S L A GI TVYQ+++L PN+SVAEN+ A R Sbjct: 72 GGQMRLGGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENI-----FAGRYPRCGIAQ 126 Query: 129 DRRVLAATA-ARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPT 187 R+ AT RA + V G + L+ P+A +QLVAIARA++ E++ +I+DEPT Sbjct: 127 GFRIDWATLHQRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPT 186 Query: 188 TSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFT 247 +SL EV L VL LR++G++++FV+H L++ YA+ + VLR+G + + + Sbjct: 187 SSLDDDEVQKLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLG 246 Query: 248 KAQISELMTGRHLSNERYR-------ESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEIL 300 + M GR L+ + +S HA +L G + Q + ++ GE++ Sbjct: 247 PQALIAAMLGRDLAAASEQPAPAPAVDSRHAN--LLQAEGLGQDTQLQPLDLQIRAGEVV 304 Query: 301 GVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGL 360 G+ GLL SGR ELAR L G+ G + +DGQ + P DA RH + PE+R +G+ Sbjct: 305 GLAGLLGSGRTELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGI 364 Query: 361 FLDKPIRDNVITAMISSLRDRFGQ---IDRTRAQALAEQTVKELQIATPGVDKPVQSLSG 417 + +R+N+ A L+ R G + R+ LAE+ VK L I T VDKP+ LSG Sbjct: 365 VAELSVRENIALA----LQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSG 420 Query: 418 GNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPEL 477 GNQQ+ ++ RW+AI+PR+LIL PT G+DV +K I + RL+Q G+ ++ IS ++ E+ Sbjct: 421 GNQQKAILARWMAIEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEV 480 Query: 478 LQNCDRILMMKKGHVSAEYRADELSEADLYHALLSEAA 515 ++ RI++++ E A SE +Y + +E A Sbjct: 481 VRVAHRIVVLRDRRKVGELPAGS-SEDAVYDLIAAEHA 517 Lambda K H 0.319 0.135 0.376 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: 621 Number of extensions: 27 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 515 Length of database: 517 Length adjustment: 35 Effective length of query: 480 Effective length of database: 482 Effective search space: 231360 Effective search space used: 231360 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 (21.7 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