Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate SM_b20673 SM_b20673 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Smeli:SM_b20673 Length = 526 Score = 380 bits (976), Expect = e-110 Identities = 212/505 (41%), Positives = 322/505 (63%), Gaps = 14/505 (2%) Query: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 L + I K F GV AL V F++ G++H LMGENGAGKSTL+K+L G Y G V +D Sbjct: 19 LAAEAISKSFGGVAALKDVRFELRAGEIHALMGENGAGKSTLMKVLSGVYTDYEGAVRVD 78 Query: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLG-WVNKREAKRFVRE 123 G VRF++ + AAGIA+IHQEL VP+L VA+N+ LG+ G +V+++ + R Sbjct: 79 GETVRFSNVRDAEAAGIAIIHQELNLVPELGVADNIFLGRERVIAGLFVDRKASLEAARG 138 Query: 124 RLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLV 183 L +G+ LDP A++ +L + ++Q+VEI KAL AR++ +DEPTS+LS E LFK++ Sbjct: 139 LLNRLGIELDPEARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSALSPGECRRLFKIM 198 Query: 184 RDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREIS 243 R L AD +IYISHR+DE+ +L D T+FRDGR + + P + G+ +TI++ MVGR + Sbjct: 199 RQLAADGVGIIYISHRIDEVMQLSDRVTVFRDGRHVWARP-MAGLDENTIIAAMVGRNLL 257 Query: 244 DIYNY-----SARPLGEVRFAAKGIEG----HALAQPASFEVRRGEIVGFFGLVGAGRSE 294 D + P+ VR + + G + + SF+VR GEI+G GL+GAGR+E Sbjct: 258 DAHRRDRGKGGGEPVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGIGGLLGAGRTE 317 Query: 295 LMHLVYGADH-KKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENIN 353 ++ ++ ++ +GGE+ LDG + +RS +A R G L EDRK +G+ ++ +N+ Sbjct: 318 ILETIFASNEGLRGGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLHLHESIRDNVA 377 Query: 354 ISCRRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAE 413 + R G+ + E A + L ++ Q LSGGNQQK ++ +WLA Sbjct: 378 LPLVGRLARFGL-RSFEGERALAKGAVDALGVRCAGTGQAAGTLSGGNQQKVVIGKWLAT 436 Query: 414 PDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQG 473 +V++LDEPTRGIDVGAK EIY++I++LA G AIV++SSELPE+L ++DRI+VM +G Sbjct: 437 GP-RVLLLDEPTRGIDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLADRILVMAEG 495 Query: 474 RISGELTRKDATEQSVLSLALPQSS 498 R +G ++R++A+E+ ++ LA P+S+ Sbjct: 496 RQTGLISREEASEERIMQLAAPRSA 520 Score = 98.6 bits (244), Expect = 5e-25 Identities = 71/249 (28%), Positives = 122/249 (48%), Gaps = 19/249 (7%) Query: 226 EGVTRDTIVSEMVGREISDIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFF 285 + + RD++ +E S RP+ +K G A + FE+R GEI Sbjct: 3 DAIPRDSVTTE------------SDRPILAAEAISKSFGGVAALKDVRFELRAGEIHALM 50 Query: 286 GLVGAGRSELMHLVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAM 345 G GAG+S LM ++ G G + +DG+ ++ + +A GI + +E +V Sbjct: 51 GENGAGKSTLMKVLSGVYTDYEGAVRVDGETVRFSNVRDAEAAGIAII---HQELNLVPE 107 Query: 346 ATVSENINISCRRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKA 405 V++NI + R + G+F+DRK E A + L I+ ++ L G QQ Sbjct: 108 LGVADNIFLG--RERVIAGLFVDRKASLEAARGLLNRLGIEL-DPEARVGQLRVGEQQLV 164 Query: 406 ILSRWLAEPDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSD 465 +++ L+ + +++I+DEPT + G ++ ++ QLA G I+ IS + EV+ +SD Sbjct: 165 EIAKALS-VEARILIMDEPTSALSPGECRRLFKIMRQLAADGVGIIYISHRIDEVMQLSD 223 Query: 466 RIVVMRQGR 474 R+ V R GR Sbjct: 224 RVTVFRDGR 232 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: 723 Number of extensions: 50 Number of successful extensions: 13 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: 526 Length adjustment: 35 Effective length of query: 477 Effective length of database: 491 Effective search space: 234207 Effective search space used: 234207 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