Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23205 Length = 517 Score = 397 bits (1021), Expect = e-115 Identities = 208/486 (42%), Positives = 313/486 (64%), Gaps = 4/486 (0%) Query: 9 NIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMIDGNEV 68 N+ K FPGV AL V V G V LMGENGAGKSTL+KI+ G YQPD+G + + G V Sbjct: 31 NVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPV 90 Query: 69 RFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLG-QLPNSLGWVNKREAKRFVRERLEA 127 F + +++ AGIA+IHQEL +P +++AEN+ +G + N L V+ E R LE Sbjct: 91 TFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMHRCTARLLER 150 Query: 128 MGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVRDLR 187 + + LDP ++ LSIA+RQMVEI KA+ ++ ++ +DEPTS+++ E LF ++ DL+ Sbjct: 151 LRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLFSIIADLK 210 Query: 188 ADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISDIYN 247 + + +IYI+H+M+E++ + D +FRDG I + + D+++S MVGRE+S ++ Sbjct: 211 SQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQ-RADSMDGDSLISMMVGRELSQLFP 269 Query: 248 YSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKG 307 +P+GE+ + + + + + SF++ GEI+G GL+G+GR+ + ++G G Sbjct: 270 VREQPIGELVLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGVTPSTG 329 Query: 308 GELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFL 367 GE+ LDG+P+++ AI G L EDRK G+ +V EN+ ++ HY+ G F+ Sbjct: 330 GEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYVGNG-FI 388 Query: 368 DRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRG 427 +K + K L++KTPS Q I LSGGNQQKA+L+RWL + +++ILDEPTRG Sbjct: 389 QQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLM-TNPRILILDEPTRG 447 Query: 428 IDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQ 487 IDVGAK EIY +I LA G A++MISSELPEVLG+SDR++VM +G + G L R +AT++ Sbjct: 448 IDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQE 507 Query: 488 SVLSLA 493 V+ LA Sbjct: 508 RVMQLA 513 Score = 84.0 bits (206), Expect = 1e-20 Identities = 67/248 (27%), Positives = 119/248 (47%), Gaps = 9/248 (3%) Query: 255 EVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDG 314 EV +KG G VR G ++ G GAG+S LM ++ G GEL L G Sbjct: 28 EVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRG 87 Query: 315 KPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKKEAE 374 KP+ + A++ GI + +E ++ +++ENI I R L +D + Sbjct: 88 KPVTFDTPLAALQAGIAMI---HQELNLMPHMSIAENIWIG--REQLNGLHMVDHGEMHR 142 Query: 375 TADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGAKH 434 R ++ L+IK Q + LS +Q +++ ++ D ++I+DEPT I Sbjct: 143 CTARLLERLRIKLDPEEQ-VGNLSIAERQMVEIAKAVSY-DSDILIMDEPTSAITETEVA 200 Query: 435 EIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATE-QSVLSLA 493 ++++I L +G I+ I+ ++ EV ++D + V R G G L R D+ + S++S+ Sbjct: 201 HLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIG-LQRADSMDGDSLISMM 259 Query: 494 LPQSSTAL 501 + + + L Sbjct: 260 VGRELSQL 267 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: 640 Number of extensions: 26 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: 517 Length adjustment: 35 Effective length of query: 477 Effective length of database: 482 Effective search space: 229914 Effective search space used: 229914 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