Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Putida:PP_2455 Length = 524 Score = 333 bits (853), Expect = 1e-95 Identities = 190/471 (40%), Positives = 288/471 (61%), Gaps = 3/471 (0%) Query: 23 VSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINAGIV 82 VS+ GEV A+ GENGAGKSTL K+I+G+ P G + Y G+ EA G+ Sbjct: 34 VSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTYRGQAYAPGSRGEAERLGVR 93 Query: 83 TVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKFMKEEFGIEIDPEEKLGKY 142 V QEL+++ L+VAEN+F+ + R +I +K++ + A M IDP+ +G+ Sbjct: 94 MVMQELNLLPTLTVAENLFLDNLPSRFGWISHKRLRQLATAAMARVGLDAIDPDTPVGEL 153 Query: 143 SIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAIIFISHRLE 202 I QQMVEIAR + VLILDEPT+ LT +E LF ++ L+ +GVAI++ISHRLE Sbjct: 154 GIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFTQIERLRARGVAIVYISHRLE 213 Query: 203 EIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLEKFYIKEAHEPGEVVLEVKN 262 E+ + ++ VLRDG+ + + I+ + ++V +MVGR+L + + G +L+V Sbjct: 214 ELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVGRELGEHIDLGRRQLGAPLLKVDK 273 Query: 263 L-SGERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYI--EGKRVEIN 319 L G++ VSF +R GEI G +GL+GAGRTEL+ I+G G I + + V I+ Sbjct: 274 LCRGDKVREVSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPPQAVSID 333 Query: 320 HPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIK 379 P A+ GI L+ EDRK GL+L SI N++L +L + + + + EK LA+ I+ Sbjct: 334 SPKAAVRAGIALITEDRKGEGLLLTQSISANIALGNLGAVSRAGVLDSEAEKALAERQIQ 393 Query: 380 TFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQ 439 IR A + V LSGGNQQKVV+ +WL ++L+ DEPTRGIDVGAK +IY ++++ Sbjct: 394 AMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAE 453 Query: 440 LAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLA 490 LA++G ++++SS+L E++ + DRIAV+S G+L SQ++++ A Sbjct: 454 LARQGKALVVVSSDLRELMLICDRIAVLSAGRLIDTFARDHWSQDQLLAAA 504 Score = 86.3 bits (212), Expect = 2e-21 Identities = 67/224 (29%), Positives = 110/224 (49%), Gaps = 5/224 (2%) Query: 271 VSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIG 330 VS SLR GE+L G GAG++ L + I G G + G+ +A G+ Sbjct: 34 VSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTYRGQAYAPGSRGEAERLGVR 93 Query: 331 LVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDR 390 +V ++ L L+ +++ N+ L +L + +IS KR ++LA A+ + PD Sbjct: 94 MVMQE---LNLLPTLTVAENLFLDNLP--SRFGWISHKRLRQLATAAMARVGLDAIDPDT 148 Query: 391 KVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMI 450 V L G+QQ V +A+ L +LILDEPT + A ++ + +L GV ++ I Sbjct: 149 PVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFTQIERLRARGVAIVYI 208 Query: 451 SSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494 S L E+ +++ RI V+ GKL + S +++ L G E Sbjct: 209 SHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVGRE 252 Score = 79.0 bits (193), Expect = 4e-19 Identities = 57/222 (25%), Positives = 113/222 (50%), Gaps = 7/222 (3%) Query: 20 LKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII--YEGRGVRWNHPSEAI 77 ++ VS E GE+ I G GAG++ L+++I G + D G I + V + P A+ Sbjct: 280 VREVSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPPQAVSIDSPKAAV 339 Query: 78 NAGIVTVFQEL---SVMDNLSVAENIFMGD--EEKRGIFIDYKKMYREAEKFMKEEFGIE 132 AGI + ++ ++ S++ NI +G+ R +D + AE+ ++ Sbjct: 340 RAGIALITEDRKGEGLLLTQSISANIALGNLGAVSRAGVLDSEAEKALAERQIQAMRIRS 399 Query: 133 IDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGV 192 ++ +G+ S QQ V I R + + +VL+ DEPT + ++ ++ L +G Sbjct: 400 AGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQGK 459 Query: 193 AIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIV 234 A++ +S L E+ ICD+++VL G I T + ++ ++++++ Sbjct: 460 ALVVVSSDLRELMLICDRIAVLSAGRLIDTFARDHWSQDQLL 501 Lambda K H 0.318 0.138 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: 601 Number of extensions: 31 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 494 Length of database: 524 Length adjustment: 34 Effective length of query: 460 Effective length of database: 490 Effective search space: 225400 Effective search space used: 225400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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