Align deoxynucleoside transporter, ATPase component (characterized)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >NCBI__GCF_003046325.1:WP_069332735.1 Length = 499 Score = 295 bits (756), Expect = 2e-84 Identities = 172/498 (34%), Positives = 282/498 (56%), Gaps = 15/498 (3%) Query: 11 LSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEG 70 +++P L + V + F V L V + G+++ L+GENG GKST +KI++G P G Sbjct: 1 MTEPVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAG 60 Query: 71 QLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDR 130 +++++G P S+ EA AAG+ ++Q+ +L ++V EN+ L EL + D Sbjct: 61 EVLLDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGREL-----KRGPFLDH 115 Query: 131 RVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSL 190 R + A + R LE + + + + L + RQ+V IA+A+ +A+ +IMDEPT L Sbjct: 116 RAMQAESRRLLERLHCAVDPRAR---VSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVL 172 Query: 191 TQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQ 250 T +E D L+ + LRA G +L+ SHKLDE I V VLRDG+++ P ++ + Sbjct: 173 THRETDTLLEQVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDR 232 Query: 251 ISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGR 310 ++E M GR LS +S+ A + VL+V G T G D SF L GE+LG GL+ SGR Sbjct: 233 MAETMVGRELSGLFPPKSSPAPEPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGR 292 Query: 311 NELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNV 370 EL + G+ PA +G+V ++G + + S A+ + Y+ EDR +GL L KP+ +N+ Sbjct: 293 TELMEGIVGLRPA-TGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENL 351 Query: 371 ITAMISSLRDRFGQ--IDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRW 428 + DRFG+ ID+ + Q + + I SLSGGNQQ++L+ + Sbjct: 352 TLLAL----DRFGRVLIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKT 407 Query: 429 LAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMK 488 + +PRV+I+ PT G+DVG+K IY + RL+ G +I++S +LPE++ +R+++M Sbjct: 408 MLAEPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMS 467 Query: 489 KGHVSAEYRADELSEADL 506 G ++ E + ++E ++ Sbjct: 468 AGRIAGEVEGEAITEENI 485 Score = 73.2 bits (178), Expect = 2e-17 Identities = 73/267 (27%), Positives = 122/267 (45%), Gaps = 42/267 (15%) Query: 8 SAPLSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPP 67 S+P +P LEV G+ T +R S + +RG++ G G G++ L++ I G +P Sbjct: 250 SSPAPEPVLEVAGL----TVPGFVRDASFTLRRGEVLGFAGLVGSGRTELMEGIVGLRPA 305 Query: 68 DEGQLVIEG--VPHARLSALEALAAGIETVYQDLS---LLPNMSVAENVALTS------- 115 G++ +EG +PHA +SA A AAG+ + +D LL + EN+ L + Sbjct: 306 T-GEVRMEGSPLPHASVSA--ARAAGLVYLTEDRKEKGLLLGKPLGENLTLLALDRFGRV 362 Query: 116 --ELATHEGRLART---FDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAI 170 + A E L + FD RV R + A L G ++ Q + + Sbjct: 363 LIDKAAEERALTQAISDFDIRV----GDRGISAGSLSGGNQ--------------QKLLL 404 Query: 171 ARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVI 230 A+ + +E + VI+DEPT + + +A L A+G +V+ VS +L E + V+ Sbjct: 405 AKTMLAEPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVV 464 Query: 231 VLRDGQKMAQGPIAEFTKAQISELMTG 257 V+ G+ + T+ I L G Sbjct: 465 VMSAGRIAGEVEGEAITEENIVRLAMG 491 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: 591 Number of extensions: 34 Number of successful extensions: 9 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: 499 Length adjustment: 34 Effective length of query: 481 Effective length of database: 465 Effective search space: 223665 Effective search space used: 223665 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