Align deoxynucleoside transporter, ATPase component (characterized)
to candidate WP_011653997.1 RL_RS23960 sugar ABC transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >NCBI__GCF_000009265.1:WP_011653997.1 Length = 513 Score = 338 bits (867), Expect = 3e-97 Identities = 177/496 (35%), Positives = 304/496 (61%), Gaps = 7/496 (1%) Query: 8 SAPLSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPP 67 + P ++ L GV K F GV AL V +R ++ L+GENG GKSTL+KI++G P Sbjct: 16 AVPNAEYLLSAEGVRKEFPGVVALDDVQFRLKRASVHALMGENGAGKSTLMKILAGIYTP 75 Query: 68 DEGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLART 127 D+G + ++G+ S L+AL GI ++Q+L+L+P M+VAEN+ + E G + Sbjct: 76 DKGDIRLKGIEIQLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNRLGFI--- 132 Query: 128 FDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPT 187 D V+ + + + + + + L +A RQ+V IA+A++ + +IMDEPT Sbjct: 133 -DHGVMHRMTEELFTRLNIAIDPDIE---VRFLSVANRQMVEIAKAVSYNSDVLIMDEPT 188 Query: 188 TSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFT 247 ++LT++EV++L ++ +L+AQG+ +++++HK++E + I E V RDG+ + + T Sbjct: 189 SALTEREVEHLFRIIRDLKAQGIGIVYITHKMNELFEIADEFSVFRDGRYIGTHASTDVT 248 Query: 248 KAQISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLD 307 + I +M GR ++ +E +++L V+ G F +VSF++ GEILGV GL+ Sbjct: 249 RDDIIRMMVGREITQMFPKEEVPIGEVMLSVKDLCLNGVFKNVSFEVRAGEILGVAGLVG 308 Query: 308 SGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIR 367 SGR+ +A L GV PA SG + L G+ +A+ +P++A R+R+ ++ EDR + G L I Sbjct: 309 SGRSNVAETLFGVTPASSGSIELYGKPVAISSPTEAIRNRMAFLTEDRKDTGCLLILDIL 368 Query: 368 DNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGR 427 +N+ A++ + G + + +A E K+L++ TP + + V++LSGGNQQ+VLIGR Sbjct: 369 ENMQIAVLQDRYVKGGFVQQGAVEATCEDMAKKLRVKTPNLYERVENLSGGNQQKVLIGR 428 Query: 428 WLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMM 487 WL +PR+LIL PT G+DVG+K I+R++ +++ G+ +++IS ++PE+L DRI++M Sbjct: 429 WLLTNPRILILDEPTRGIDVGAKAEIHRLVTEMARDGVAVVMISSEMPEVLGMSDRIMVM 488 Query: 488 KKGHVSAEYRADELSE 503 +G V+ DE ++ Sbjct: 489 HEGRVTGFLNRDEATQ 504 Score = 79.3 bits (194), Expect = 3e-19 Identities = 58/223 (26%), Positives = 110/223 (49%), Gaps = 6/223 (2%) Query: 289 DVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRI 348 DV F+L + + G +G++ L + LAG+ GD+ L G +I L++P DA + I Sbjct: 41 DVQFRLKRASVHALMGENGAGKSTLMKILAGIYTPDKGDIRLKGIEIQLKSPLDALENGI 100 Query: 349 GYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGV 408 + ++ LN F+ + +N+ ++R G ID + E+ L IA Sbjct: 101 AMIHQE-LNLMPFMT--VAENIWIRR--EPKNRLGFIDHGVMHRMTEELFTRLNIAIDP- 154 Query: 409 DKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGII 468 D V+ LS N+Q V I + ++ + VLI+ PT + + ++RI++ L +GIGI+ Sbjct: 155 DIEVRFLSVANRQMVEIAKAVSYNSDVLIMDEPTSALTEREVEHLFRIIRDLKAQGIGIV 214 Query: 469 LISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADLYHALL 511 I+ + EL + D + + G + + +++ D+ ++ Sbjct: 215 YITHKMNELFEIADEFSVFRDGRYIGTHASTDVTRDDIIRMMV 257 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: 588 Number of extensions: 34 Number of successful extensions: 6 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: 515 Length of database: 513 Length adjustment: 35 Effective length of query: 480 Effective length of database: 478 Effective search space: 229440 Effective search space used: 229440 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 24 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