Align deoxynucleoside transporter, ATPase component (characterized)
to candidate WP_011842381.1 RSPH17029_RS17460 sugar ABC transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >NCBI__GCF_000015985.1:WP_011842381.1 Length = 497 Score = 399 bits (1024), Expect = e-115 Identities = 221/501 (44%), Positives = 330/501 (65%), Gaps = 9/501 (1%) Query: 11 LSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEG 70 +S +E+ + KRF GV AL GVSL+ + G+I+ L GENG GKST+IK++SG P+EG Sbjct: 1 MSDTLIELRNIGKRFGGVRALDGVSLAIRPGEIHCLAGENGSGKSTVIKVMSGIYTPEEG 60 Query: 71 QLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDR 130 +++I+G P RL + A+ G++ +YQD SL N++VAEN+AL + + EGR R D Sbjct: 61 EILIDGRPVGRLDPIRAVQHGVQVIYQDFSLFGNLTVAENLALNTYVL--EGR--RRMDW 116 Query: 131 RVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSL 190 R A L +G+ + + + + LP + RQ+VAIARAI ++A+ +IMDEPTT+L Sbjct: 117 RRARTMAVEVLARLGVDIDPDAE---VGTLPTSGRQVVAIARAILAKARLIIMDEPTTAL 173 Query: 191 TQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQ 250 T+ EVD L A++ +L+AQG+ VLFVSHK+ E I + V R+G+K+A+GP+++F +A Sbjct: 174 TRHEVDALFAIVRDLQAQGIAVLFVSHKMREMLEISERLTVFRNGRKVAEGPMSDFDEAA 233 Query: 251 ISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGR 310 I+ MTG L+++ YR + +L+VR + G D+ L GEI+G++GL+ SGR Sbjct: 234 ITHAMTGLSLTDDPYRPALPPGPPLLEVRKLSVPGSVQDIDLSLRPGEIVGISGLIGSGR 293 Query: 311 NELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNV 370 ELARAL G+ PA +G + L+G++I R+ +A I YVPEDRL EGLFL + I N+ Sbjct: 294 TELARALFGMEPAMTGTLRLEGREIHPRSVQEAIALGIAYVPEDRLTEGLFLPQSIERNL 353 Query: 371 ITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLA 430 + +++ LR R +D + +++QIA P + V +LSGGN QRV++GRWL Sbjct: 354 VVSILERLR-RGPFLDTGAVREKTLGMFRDMQIAAPSPETAVGNLSGGNAQRVMLGRWLL 412 Query: 431 IDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQR-GIGIILISDDLPELLQNCDRILMMKK 489 RVLIL+GPTVGVDVGSK I+RI++ L+QR G+G+++ISDD+PEL+ NC+RI +M + Sbjct: 413 TGARVLILNGPTVGVDVGSKATIHRIIRDLAQREGLGVLMISDDVPELVTNCNRIHVMHR 472 Query: 490 GHVSAEYRADELSEADLYHAL 510 G A+ ++E + AL Sbjct: 473 GRFVADLDGSGMTEDRINDAL 493 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: 625 Number of extensions: 29 Number of successful extensions: 7 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: 497 Length adjustment: 34 Effective length of query: 481 Effective length of database: 463 Effective search space: 222703 Effective search space used: 222703 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 Apr 10 2024. 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