Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate SM_b20713 SM_b20713 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Smeli:SM_b20713 Length = 513 Score = 414 bits (1065), Expect = e-120 Identities = 214/490 (43%), Positives = 323/490 (65%), Gaps = 3/490 (0%) Query: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 L + + K FPGV ALD V F + G VH LMGENGAGKSTL+KIL G Y PD G V + Sbjct: 24 LTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVKLR 83 Query: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLP-NSLGWVNKREAKRFVRE 123 G +R S ++ GIA+IHQEL +P +TVAEN+ + + P N G+V+ E +R + Sbjct: 84 GAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNRFGFVDHGEMRRMTAK 143 Query: 124 RLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLV 183 E + + LDP ++R LS+A RQMVEI KA+ + V+ +DEPTS+L+ RE LF+++ Sbjct: 144 LFERLKIDLDPEIEVRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLFEII 203 Query: 184 RDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREIS 243 RDLR+ ++YI+H+M+E++E+ D ++FRDG+ I +H + E VTRD I+ MVGREI+ Sbjct: 204 RDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNE-VTRDDIIRMMVGREIT 262 Query: 244 DIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGAD 303 ++ P+G+V + K + + + + SF+VR GEI+G GLVG+GRS + ++G Sbjct: 263 QMFPKEEVPIGDVVLSVKNLTLNGVFRDVSFDVRAGEILGVAGLVGSGRSNVAETLFGVT 322 Query: 304 HKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRV 363 G + +DGK + + SA +AIRH + EDRK+ G + + + EN+ I+ + Sbjct: 323 PASSGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTGCLLILDILENMQIAVLQDKFVK 382 Query: 364 GMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDE 423 F+ ++ + + L++KTP+ ++++ LSGGNQQK ++ RWL + +++ILDE Sbjct: 383 RGFVSEREVTAACEEMSRKLRVKTPNLQERVENLSGGNQQKVLIGRWLL-TNPRILILDE 441 Query: 424 PTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKD 483 PTRGIDVGAK EI+ ++ +LA G A++MISSE+PEVLG+SDRI+VM +GR++G L R + Sbjct: 442 PTRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMSDRIMVMHEGRVTGILDRAE 501 Query: 484 ATEQSVLSLA 493 AT+ V+ LA Sbjct: 502 ATQIKVMELA 511 Score = 84.7 bits (208), Expect = 7e-21 Identities = 66/256 (25%), Positives = 122/256 (47%), Gaps = 11/256 (4%) Query: 250 ARPLGEVRFAAKGIE----GHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHK 305 A P E A+G+ G F+++RG + G GAG+S LM ++ G + Sbjct: 16 AVPKSEYLLTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYP 75 Query: 306 KGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGM 365 GE+ L G I+++S +A+ +GI + +E ++ TV+ENI I R R G Sbjct: 76 DQGEVKLRGAGIRLKSPLDALENGIAMI---HQELNLMPFMTVAENIWIR-REPKNRFG- 130 Query: 366 FLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPT 425 F+D + + + LKI + +R LS N+Q +++ ++ + V+I+DEPT Sbjct: 131 FVDHGEMRRMTAKLFERLKIDLDPEIE-VRHLSVANRQMVEIAKAVSY-ESDVLIMDEPT 188 Query: 426 RGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDAT 485 + ++ +I L +G IV I+ ++ E+ ++D V R G+ G + T Sbjct: 189 SALTEREVAHLFEIIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVT 248 Query: 486 EQSVLSLALPQSSTAL 501 ++ + + + T + Sbjct: 249 RDDIIRMMVGREITQM 264 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: 33 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: 513 Length adjustment: 35 Effective length of query: 477 Effective length of database: 478 Effective search space: 228006 Effective search space used: 228006 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