Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Cola:Echvi_1282 Length = 502 Score = 375 bits (964), Expect = e-108 Identities = 205/501 (40%), Positives = 316/501 (63%), Gaps = 12/501 (2%) Query: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 L NI K F GV+ALD VS ++ G+V ++GENGAGKSTL+KIL G Y G + + Sbjct: 2 LTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYYN 61 Query: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNS-LGWVNKREAKRFVRE 123 G+ V+F + + GI +IHQEL +P L++ EN+ LG+ P + +G ++ + + + Sbjct: 62 GDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEAAQ 121 Query: 124 RLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLV 183 L + + +DP + +L + Q+Q+VEI KAL ++VI +DEPTS++S +E E+LF ++ Sbjct: 122 LLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGII 181 Query: 184 RDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREIS 243 R LRA+ +A+ YISH++DE++ + D + RDG+ I S +EG+T + ++ +MVGREI Sbjct: 182 RALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIES-GEMEGMTEEALIQKMVGREIV 240 Query: 244 DIYNYSARPLGEVRFAAK-------GIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELM 296 + S R E + K I L Q +FE+ +GE++G FGL+GAGR+ELM Sbjct: 241 IERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTELM 300 Query: 297 HLVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISC 356 ++G +G E+ L GK + + EA+ G+ L PEDRK++G+V + N +++ Sbjct: 301 EALFGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSSLTV 360 Query: 357 RRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDL 416 L G+ LD KKE A +++ LKIK S RQ + LSGGNQQK +L++WLA Sbjct: 361 VDSILSGGL-LDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWLATRP- 418 Query: 417 KVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRIS 476 KV++LDEPTRGID+ AK+EIY +I QLA G ++++SSELPE+L VSDR++VM +GR++ Sbjct: 419 KVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEGRLT 478 Query: 477 GEL-TRKDATEQSVLSLALPQ 496 + +E +L A+P+ Sbjct: 479 ANIPIDAQTSEDEILQAAIPK 499 Score = 77.8 bits (190), Expect = 9e-19 Identities = 53/228 (23%), Positives = 106/228 (46%), Gaps = 6/228 (2%) Query: 20 LDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMIDGNEVRFTSAASSIAA 79 L ++F++ G+V G+ G GAG++ L++ L G + + G F ++ A Sbjct: 273 LQDINFELGKGEVLGIFGLMGAGRTELMEALFGVLPHQGAEITLAGKVHEFQKPQEAMDA 332 Query: 80 GIAVIHQE-----LQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRERLEAMGVALDP 134 G+A++ ++ L DL +L + S G ++ ++ K ++ + + + Sbjct: 333 GLALVPEDRKQDGLVLCMDLCTNSSLTVVDSILSGGLLDDKKEKGLAQKYMGELKIKASS 392 Query: 135 NAKL-RKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVRDLRADNRAM 193 + +L KLS +Q V + K L +V+ LDEPT + ++KL+R L + + Sbjct: 393 HRQLVEKLSGGNQQKVVLAKWLATRPKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGL 452 Query: 194 IYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGRE 241 I +S + EI + D + +GR A+ P + D I+ + ++ Sbjct: 453 IVVSSELPEILAVSDRVLVMAEGRLTANIPIDAQTSEDEILQAAIPKK 500 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: 666 Number of extensions: 41 Number of successful extensions: 10 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: 502 Length adjustment: 34 Effective length of query: 478 Effective length of database: 468 Effective search space: 223704 Effective search space used: 223704 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