Align deoxynucleoside transporter, ATPase component (characterized)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 304 bits (778), Expect = 6e-87 Identities = 180/492 (36%), Positives = 286/492 (58%), Gaps = 13/492 (2%) Query: 9 APLSQPF-LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPP 67 +P ++P L+ G+ KRF AL GV L+ + G+++ L+G+NG GKSTLIK+++G + P Sbjct: 5 SPAARPVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERP 64 Query: 68 DEGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLART 127 D G + ++G A + +EA GI TVYQ+++L PN+SVAEN L + RL R Sbjct: 65 DRGSVELDGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAEN--LYAGRYPRRRRL-RM 121 Query: 128 FDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPT 187 D R + A L + L + + + P+A RQ+VAIARA+ A+ +I+DEPT Sbjct: 122 IDWRQVRDGARSLLRQLHLELDVDAP---LGSYPVAIRQMVAIARALGVSARVLILDEPT 178 Query: 188 TSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFT 247 +SL + EV L V+A LR +G+ +LFV+H LD+ YA+ + VLRDG ++ + +A+ Sbjct: 179 SSLDEGEVRELFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLP 238 Query: 248 KAQISELMTGRHLSNERYRESAHA----QDIVLDVRGFTRAGQFSDVSFKLHGGEILGVT 303 A + M GR L ++ A +D +G G+ V ++ GE+LG+ Sbjct: 239 PAALVNAMVGRDLPTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLG 298 Query: 304 GLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLD 363 GLL SGR ELAR L G+ A+ G++ + G+++ L+ P+DA + PE+R +G+ + Sbjct: 299 GLLGSGRTELARLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAE 358 Query: 364 KPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRV 423 +R+N++ A+ R + + R R LA Q V+ L I ++ PV LSGGNQQ+V Sbjct: 359 LSVRENIVLAL--QARQGWRGMSRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKV 416 Query: 424 LIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDR 483 ++ RWL +PR+LIL PT G+DV +K + + R + G+ ++ IS + EL + CDR Sbjct: 417 MLARWLVTEPRLLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDR 476 Query: 484 ILMMKKGHVSAE 495 I +M++ + E Sbjct: 477 IAVMRERRKAGE 488 Score = 94.0 bits (232), Expect = 1e-23 Identities = 73/248 (29%), Positives = 119/248 (47%), Gaps = 9/248 (3%) Query: 268 SAHAQDIVLDVRG----FTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPA 323 S A+ +VL RG F V L GE+ + G +G++ L + L GV Sbjct: 5 SPAARPVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERP 64 Query: 324 QSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFG 383 G V LDG+ IA TP +A+R IG V ++ L + + +N+ R R Sbjct: 65 DRGSVELDGRVIAPSTPMEAQRDGIGTVYQE---VNLCPNLSVAENLYAGRYPRRR-RLR 120 Query: 384 QIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTV 443 ID + + A +++L + VD P+ S +Q V I R L + RVLIL PT Sbjct: 121 MIDWRQVRDGARSLLRQLHLELD-VDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTS 179 Query: 444 GVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSE 503 +D G ++R++ +L +RG+ I+ ++ L ++ DRI +++ G EY +L Sbjct: 180 SLDEGEVRELFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPP 239 Query: 504 ADLYHALL 511 A L +A++ Sbjct: 240 AALVNAMV 247 Score = 62.0 bits (149), Expect = 5e-14 Identities = 59/231 (25%), Positives = 106/231 (45%), Gaps = 12/231 (5%) Query: 31 LRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEG----VPHARLSALE 86 L V L +RG++ L G G G++ L +++ G + G+L I G + H + + Sbjct: 282 LHPVDLQVRRGEMLGLGGLLGSGRTELARLLFGLDRAERGELRIGGERVELKHPADAVVR 341 Query: 87 ALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAATAARALEAVGL 146 LA E D ++ +SV EN+ L L +G R R A + ++A+G+ Sbjct: 342 GLALCPEERKTD-GIVAELSVRENIVLA--LQARQGW--RGMSRARQDELARQLVQALGI 396 Query: 147 PGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLR 206 T + L +Q V +AR + +E + +I+DEPT + L+A + Sbjct: 397 KAADI--ETPVGLLSGGNQQKVMLARWLVTEPRLLILDEPTRGIDVAAKQELMAEVTRRA 454 Query: 207 AQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTG 257 G+ VLF+S + E + V+R+ +K + P T+A++ ++ G Sbjct: 455 HAGMAVLFISAETGELTRWCDRIAVMRERRKAGELP-GGSTEARVLAMIAG 504 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: 601 Number of extensions: 29 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 515 Length of database: 505 Length adjustment: 34 Effective length of query: 481 Effective length of database: 471 Effective search space: 226551 Effective search space used: 226551 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 09 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