Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 321 bits (823), Expect = 3e-92 Identities = 189/495 (38%), Positives = 291/495 (58%), Gaps = 13/495 (2%) Query: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 L+ +GK F ALDGV + G+VH LMG+NGAGKSTL+K+L G +PD G V +D Sbjct: 13 LQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVELD 72 Query: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLP--NSLGWVNKREAKRFVR 122 G + ++ + GI ++QE+ P+L+VAENL G+ P L ++ R+ + R Sbjct: 73 GRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDGAR 132 Query: 123 ERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKL 182 L + + LD +A L +A RQMV I +AL +ARV+ LDEPTSSL E LF++ Sbjct: 133 SLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELFRV 192 Query: 183 VRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREI 242 + LR A+++++H +D++Y + D T+ RDG ++ + + + +V+ MVGR++ Sbjct: 193 IAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVAD-LPPAALVNAMVGRDL 251 Query: 243 SDIYNYSAR----PLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHL 298 + A P A+G+ P +VRRGE++G GL+G+GR+EL L Sbjct: 252 PTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGRTELARL 311 Query: 299 VYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRR 358 ++G D + GEL + G+ ++++ +A+ G+ LCPE+RK +GIVA +V ENI ++ + Sbjct: 312 LFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVRENIVLALQA 371 Query: 359 HYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWL-AEPDLK 417 GM R ++ E A + ++ L IK + LSGGNQQK +L+RWL EP + Sbjct: 372 RQGWRGM--SRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWLVTEP--R 427 Query: 418 VVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISG 477 ++ILDEPTRGIDV AK E+ + + A G A++ IS+E E+ DRI VMR+ R +G Sbjct: 428 LLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERRKAG 487 Query: 478 ELTRKDATEQSVLSL 492 EL +TE VL++ Sbjct: 488 ELP-GGSTEARVLAM 501 Score = 87.0 bits (214), Expect = 1e-21 Identities = 79/260 (30%), Positives = 123/260 (47%), Gaps = 18/260 (6%) Query: 250 ARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGE 309 AR LG+ A ++G LA +R GE+ G GAG+S L+ L+ G + G Sbjct: 15 ARGLGKRFGATLALDGVDLA------LRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGS 68 Query: 310 LLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISC--RRHYLRVGMFL 367 + LDG+ I + EA R GI + E + +V+EN+ RR LR+ + Sbjct: 69 VELDGRVIAPSTPMEAQRDGIGTVYQ---EVNLCPNLSVAENLYAGRYPRRRRLRMIDWR 125 Query: 368 DRKKEAETADRFIKL-LKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTR 426 + A + R + L L + P + +Q ++R L +V+ILDEPT Sbjct: 126 QVRDGARSLLRQLHLELDVDAPLGSYPVAI-----RQMVAIARALGV-SARVLILDEPTS 179 Query: 427 GIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATE 486 +D G E++ VI QL ERG AI+ ++ L +V VSDRI V+R G GE D Sbjct: 180 SLDEGEVRELFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPP 239 Query: 487 QSVLSLALPQSSTALPGTQA 506 ++++ + + + G A Sbjct: 240 AALVNAMVGRDLPTVAGADA 259 Lambda K H 0.320 0.136 0.385 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: 667 Number of extensions: 38 Number of successful extensions: 8 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: 512 Length of database: 505 Length adjustment: 34 Effective length of query: 478 Effective length of database: 471 Effective search space: 225138 Effective search space used: 225138 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 (21.8 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