Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__azobra:AZOBR_RS31210 Length = 516 Score = 365 bits (938), Expect = e-105 Identities = 209/505 (41%), Positives = 310/505 (61%), Gaps = 20/505 (3%) Query: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 L + K F GV+ALDGV F V G++H L+GENGAGKSTL+K L G YQ D+G V ++ Sbjct: 13 LAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVTLE 72 Query: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124 G + + I ++QE+ +P+L+VAENL LG+ P G V++ +R R Sbjct: 73 GRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFGLVDRGAMRRRARAV 132 Query: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184 L G+ LD A L + S+A +Q+V I +A+ +A+V+ LDEPT+SL +E VLFK++R Sbjct: 133 LIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAVLFKVMR 192 Query: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244 LR+ +++++H +D++Y LCD T+ R+GR + T E + R +V+ M+GRE+ Sbjct: 193 TLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAE-LPRLDLVAMMLGRELEA 251 Query: 245 IYNYSARPLGE---------VRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSEL 295 + + A P + VRF +G +P ++R GE+VG GL+G+GR+E Sbjct: 252 VAHRIAPPADDAEEDARPPLVRF--RGYGKARSVEPFDLDIRPGEVVGLAGLLGSGRTET 309 Query: 296 MHLVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENI--N 353 LV+G D GE +DG+ +++R +AIR G CPEDRK+EGIV +V ENI Sbjct: 310 ARLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRENIILA 369 Query: 354 ISCRRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLA- 412 + R+ +LR + R ++ E ADRFI+LL I+TP Q I+ LSGGNQQKA+L+RWLA Sbjct: 370 LQARQGWLRP---IPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWLAT 426 Query: 413 EPDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQ 472 EP +++ILDEPTRGIDVGA EI +I +L G A++++SSEL E++ S R+VV+R Sbjct: 427 EP--RLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRD 484 Query: 473 GRISGELTRKDATEQSVLSLALPQS 497 R EL + +++ +S Sbjct: 485 RRHVAELRGGEVAVDRIVAAIASES 509 Score = 81.3 bits (199), Expect = 8e-20 Identities = 70/253 (27%), Positives = 113/253 (44%), Gaps = 14/253 (5%) Query: 252 PLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELL 311 PL +R +K G F VR GEI G GAG+S L+ + G + G + Sbjct: 11 PLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVT 70 Query: 312 LDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMF---LD 368 L+G+ I R EA R I + E ++ +V+EN+ + R +R G+ Sbjct: 71 LEGRAIAPRGVEEAQRLHIGTVYQ---EVNLLPNLSVAENLFLG--RQPMRFGLVDRGAM 125 Query: 369 RKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGI 428 R++ + L + P R S QQ ++R + KV+ILDEPT + Sbjct: 126 RRRARAVLIPYGLTLDVTAPLGR-----FSVATQQIVAIAR-AVDMSAKVLILDEPTASL 179 Query: 429 DVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQS 488 D ++ V+ L RG IV ++ L +V + DRI V+R GR+ GE + Sbjct: 180 DAQEVAVLFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLD 239 Query: 489 VLSLALPQSSTAL 501 ++++ L + A+ Sbjct: 240 LVAMMLGRELEAV 252 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: 662 Number of extensions: 29 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: 516 Length adjustment: 35 Effective length of query: 477 Effective length of database: 481 Effective search space: 229437 Effective search space used: 229437 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