Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate H281DRAFT_00426 H281DRAFT_00426 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Burk376:H281DRAFT_00426 Length = 503 Score = 413 bits (1062), Expect = e-120 Identities = 223/496 (44%), Positives = 320/496 (64%), Gaps = 5/496 (1%) Query: 1 MSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR 60 M+ + + K FPGVRAL V FD+ G+VH LMGENGAGKSTL+KIL G Y DSG Sbjct: 1 MTPLISVKKLSKSFPGVRALHDVQFDLVEGEVHALMGENGAGKSTLMKILAGVYTRDSGE 60 Query: 61 VMIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNS-LG-WVNKREAK 118 +++ G V S + AAGI +IHQELQ + LTVA+N+ +G+ P LG ++++ + Sbjct: 61 ILLGGQPVELQSPRDAQAAGIGIIHQELQLMNHLTVAQNIFIGREPRGRLGLFLDEDKLN 120 Query: 119 RFVRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEV 178 RE L M V +DP A + L++A +QMVEI KAL ++RV+ +DEPTS+L+ E Sbjct: 121 AKAREILSRMHVNIDPRAMVGNLTVASQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAE 180 Query: 179 LFKLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMV 238 LF+++R+L+ ++YISH+MDE+ ++ D T+ RDG +A+ + + + I+ MV Sbjct: 181 LFRIIRELKQRGVGVVYISHKMDELKQIADRVTVLRDGEYVATVAAAD-TSVEAIIGMMV 239 Query: 239 GREISDIYNYS-ARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMH 297 GR +SD+ A GE+ + + L + SF +R+GEI+GF GL+GAGR+E+ Sbjct: 240 GRTLSDVAPAGRAASQGEIALEVRNLHAGPLVRDVSFTLRKGEILGFAGLMGAGRTEVAR 299 Query: 298 LVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCR 357 V+GAD + GE+ + G +R+ +A+ HGI EDRK G+ V NI +S Sbjct: 300 AVFGADPVESGEIFVKGAKASIRTPSDAVAHGIGYLSEDRKRFGLATGMDVESNIVMSNL 359 Query: 358 RHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLK 417 R++L + FL R + A FI LL I+TPS Q++R LSGGNQQK ++++WL E D Sbjct: 360 RNFLSLNFFLRRARMRRRASHFINLLAIRTPSAAQQVRLLSGGNQQKIVIAKWL-ERDCD 418 Query: 418 VVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISG 477 V+ DEPTRGIDVGAK EIY ++ LA+ G AIVMISSELPE+L +SDR+VVM +GRI+G Sbjct: 419 VLFFDEPTRGIDVGAKSEIYKLLRSLADEGKAIVMISSELPEILRMSDRVVVMCEGRITG 478 Query: 478 ELTRKDATEQSVLSLA 493 EL + AT++ ++ LA Sbjct: 479 ELPAEQATQERIMHLA 494 Score = 105 bits (262), Expect = 4e-27 Identities = 71/259 (27%), Positives = 137/259 (52%), Gaps = 7/259 (2%) Query: 252 PLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELL 311 PL V+ +K G F++ GE+ G GAG+S LM ++ G + GE+L Sbjct: 3 PLISVKKLSKSFPGVRALHDVQFDLVEGEVHALMGENGAGKSTLMKILAGVYTRDSGEIL 62 Query: 312 LDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKK 371 L G+P++++S +A GI + ++ + ++ TV++NI I R R+G+FLD K Sbjct: 63 LGGQPVELQSPRDAQAAGIGIIHQELQ---LMNHLTVAQNIFIG-REPRGRLGLFLDEDK 118 Query: 372 EAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVG 431 A + + + R + L+ +QQ +++ L+ D +V+I+DEPT ++ Sbjct: 119 LNAKAREILSRMHVNIDPRAM-VGNLTVASQQMVEIAKALSF-DSRVLIMDEPTSALNDA 176 Query: 432 AKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLS 491 E++ +I +L +RG +V IS ++ E+ ++DR+ V+R G + D + ++++ Sbjct: 177 EIAELFRIIRELKQRGVGVVYISHKMDELKQIADRVTVLRDGEYVATVAAADTSVEAIIG 236 Query: 492 LALPQS-STALPGTQAAAQ 509 + + ++ S P +AA+Q Sbjct: 237 MMVGRTLSDVAPAGRAASQ 255 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: 627 Number of extensions: 36 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: 512 Length of database: 503 Length adjustment: 34 Effective length of query: 478 Effective length of database: 469 Effective search space: 224182 Effective search space used: 224182 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 Sep 17 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