Align deoxynucleoside transporter, ATPase component (characterized)
to candidate HSERO_RS05175 HSERO_RS05175 sugar ABC transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__HerbieS:HSERO_RS05175 Length = 516 Score = 333 bits (854), Expect = 9e-96 Identities = 192/517 (37%), Positives = 296/517 (57%), Gaps = 22/517 (4%) Query: 12 SQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQ 71 ++P LE+ G+HK F GV AL V L G+++ L+G+NG GKSTLIK+++G PD G+ Sbjct: 9 ARPMLELSGIHKAFAGVKALTDVGLRLFPGEVHTLMGQNGAGKSTLIKVLTGVHEPDGGK 68 Query: 72 LVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRR 131 + ++G A S LEA A GI TVYQ+++L PN+SVAEN+ T GR+ D + Sbjct: 69 IELDGRAIAPASTLEAQALGISTVYQEVNLCPNLSVAENI-FVGRYPTRFGRI----DWK 123 Query: 132 VLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLT 191 + + + L+ + + + + + PLA +Q+VAI+RA++ AK +I+DEPT+SL Sbjct: 124 SVHTQSRQLLQQLQIDID---VAAPLSSYPLAIQQMVAISRALSVSAKVLILDEPTSSLD 180 Query: 192 QKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQI 251 + EV L VL LR QG+ +LFV+H LD+ Y I + VLR+G + + ++E ++ + Sbjct: 181 EAEVQQLFKVLRRLREQGMAILFVTHFLDQTYEISDRITVLRNGVREGEYLVSELSRLDL 240 Query: 252 SELMTG-------------RHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGE 298 M G L++E ++A A + L GF R G + +L GE Sbjct: 241 VNKMVGVTAVDHRKVEAGAEALASELSTDAAAAGAVFLQAEGFGRRGVLAPQDLQLRRGE 300 Query: 299 ILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNE 358 + G+ GLL SGR E+AR L G A G + ++G+++ L P DA IG+ EDR E Sbjct: 301 VFGLCGLLGSGRTEMARLLFGADRADCGQLRIEGKEVRLNVPRDAIAAGIGFCSEDRKKE 360 Query: 359 GLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGG 418 G L+ +R+N+I A + + + F + R R +A VK L I T ++ P+ LSGG Sbjct: 361 GAILELSVRENIILA-LQARQGLFRVLPRKRQNQIAADYVKWLGIKTADLETPIGLLSGG 419 Query: 419 NQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELL 478 NQQ+ L+ RWLA DP +LIL PT G+DV +K I + + ++G+ I+ IS ++PE+L Sbjct: 420 NQQKALLARWLATDPGMLILDEPTRGIDVRAKQEIMDFVIAMCRKGMSILFISSEIPEVL 479 Query: 479 QNCDRILMMKKGHVSAEYRADELSEADLYHALLSEAA 515 + DR+L+++ EYR EL E + + E A Sbjct: 480 RCSDRMLVLRDRRACGEYRRGELDEQSVLQVIAGETA 516 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: 583 Number of extensions: 34 Number of successful extensions: 9 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: 516 Length adjustment: 35 Effective length of query: 480 Effective length of database: 481 Effective search space: 230880 Effective search space used: 230880 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