RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780342|ref|YP_003064755.1| substrate-binding region of ABC-type glycine betaine transport system [Candidatus Liberibacter asiaticus str. psy62] (309 letters) >gnl|CDD|132455 TIGR03414, ABC_choline_bnd, choline ABC transporter, periplasmic binding protein. Partial phylogenetic profiling (PubMed:16930487) vs. the genome property of glycine betaine biosynthesis from choline consistently reveals a member of this ABC transporter periplasmic binding protein as the best match, save for the betaine biosynthesis enzymes themselves. Genomes often carry several paralogs, one encoded together with the permease and ATP-binding components and another encoded next to a choline-sulfatase gene, suggesting that different members of this protein family interact with shared components and give some flexibility in substrate. Of two members from Sinorhizobium meliloti 1021, one designated ChoX has been shown experimentally to bind choline (though not various related compounds such as betaine) and to be required for about 60 % of choline uptake. Members of this protein have an invariant Cys residue near the N-terminus and likely are lipoproteins. Length = 290 Score = 390 bits (1003), Expect = e-109 Identities = 136/283 (48%), Positives = 192/283 (67%), Gaps = 3/283 (1%) Query: 19 ARDADSCTPVRFADTGWTDIAATTAMTSVILEEILGYKTNIKLLAVPVTFRSLKNKGIDI 78 A + SC VRFAD GWTDI ATTA+ SV+LE LGY+ + LL+VPVT+ LK+ +D+ Sbjct: 1 AAEPASCKTVRFADVGWTDITATTALASVLLEG-LGYQPKVTLLSVPVTYAGLKDGDLDV 59 Query: 79 FMGYWYPSLEKFIAPYLEEGSIKLVAENLQGAKYMLAVNDVGFALGIKSYQDIAKYKKEL 138 F+G W P++E I PYLE GS++++ NL+GAKY LAV G+KS+ DIAK+K +L Sbjct: 60 FLGNWMPAMEPDIKPYLESGSVEVLGPNLEGAKYTLAVPTYVADAGLKSFADIAKFKDKL 119 Query: 139 GAKIYGIEPGNEGNQRILDMINNNKFSLKGFRLIEASELASFSQIRRDQRNNIPAVFLSW 198 KIYGIEPGN+GN+ I MI+ N F L GF+L+E+SE +Q+ R + VFL W Sbjct: 120 DGKIYGIEPGNDGNRLIQKMIDKNAFGLGGFKLVESSEAGMLAQVARAVKRKEWVVFLGW 179 Query: 199 EPHPINSDLNIHYLPGGEEISG--FGEASVYTVVRSDYLDKCPNISRLLKNIKFSVALEN 256 EPHP+N++ + YL GG++ G +G A+VYT R Y +CPN+ +LL N+ F++ +EN Sbjct: 180 EPHPMNTNFKMTYLTGGDDYFGPNYGGATVYTNTRKGYAAECPNVGKLLTNLTFTLDMEN 239 Query: 257 EMMKLILNNKQDRQFVGRTMLRTHPDLLKNWLIGVTTFDGQDP 299 ++M ILN+ +D + R L+ +P++L WL GVTT DG+D Sbjct: 240 QIMGAILNDGKDPEAAARQWLKANPEVLDPWLAGVTTVDGKDG 282 >gnl|CDD|172200 PRK13652, cbiO, cobalt transporter ATP-binding subunit; Provisional. Length = 277 Score = 31.7 bits (72), Expect = 0.24 Identities = 16/52 (30%), Positives = 26/52 (50%) Query: 38 IAATTAMTSVILEEILGYKTNIKLLAVPVTFRSLKNKGIDIFMGYWYPSLEK 89 I A + + L+ L + ++ L ++P RSL+ +GI I M Y Y E Sbjct: 216 IVAYGTVEEIFLQPDLLARVHLDLPSLPKLIRSLQAQGIAIDMAYTYQEAED 267 >gnl|CDD|130383 TIGR01316, gltA, glutamate synthase (NADPH), homotetrameric. This protein is homologous to the small subunit of NADPH and NADH forms of glutamate synthase as found in eukaryotes and some bacteria. This protein is found in numerous species having no homolog of the glutamate synthase large subunit. The prototype of the family, from Pyrococcus sp. KOD1, was shown to be active as a homotetramer and to require NADPH. Length = 449 Score = 30.2 bits (68), Expect = 0.64 Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 5/68 (7%) Query: 66 VTFRSLKNKGIDIFMGYWYPSLEKFIAPYLEEGSIKLVAENLQGAKYMLAVNDVGFALGI 125 + K+ G + +G +LE+F+A + + I+ E +AV G A G+ Sbjct: 92 TVGKMFKDVGKPVSIG----ALERFVADWERQHGIETEPEKAPSTHKKVAVIGAGPA-GL 146 Query: 126 KSYQDIAK 133 ++AK Sbjct: 147 ACASELAK 154 >gnl|CDD|178068 PLN02449, PLN02449, ferrochelatase. Length = 485 Score = 29.4 bits (66), Expect = 1.4 Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 4/38 (10%) Query: 70 SLKNKG----IDIFMGYWYPSLEKFIAPYLEEGSIKLV 103 +L+ K + + M YW+P E+ I +G KLV Sbjct: 172 ALEAKNLPAKVYVGMRYWHPFTEEAIDQIKADGITKLV 209 >gnl|CDD|181713 PRK09230, PRK09230, cytosine deaminase; Provisional. Length = 426 Score = 27.4 bits (61), Expect = 5.1 Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 10/65 (15%) Query: 136 KELGAKIYGIEPGNEGNQRILDMINN---------NKFSLKGFRLIEASELASFSQIRRD 186 + L + YGIE GN N IL N ++S++ ++I ++ A + I + Sbjct: 359 RTLNLQDYGIEVGNPANLIILPAENGFDAVRRQVPVRYSIRHGKVIAETQPA-QTTIYLE 417 Query: 187 QRNNI 191 Q + Sbjct: 418 QPEAV 422 >gnl|CDD|184443 PRK13992, minC, septum formation inhibitor; Provisional. Length = 205 Score = 27.0 bits (60), Expect = 5.8 Identities = 14/44 (31%), Positives = 21/44 (47%) Query: 120 GFALGIKSYQDIAKYKKELGAKIYGIEPGNEGNQRILDMINNNK 163 G L IK YQ++ E+ AKI + +I MI N++ Sbjct: 10 GLVLLIKDYQNLEDVLNEIDAKITQMGGFFAKGDKISLMIENHE 53 >gnl|CDD|180263 PRK05799, PRK05799, coproporphyrinogen III oxidase; Provisional. Length = 374 Score = 26.9 bits (60), Expect = 6.4 Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 7/68 (10%) Query: 119 VGFALGIKSYQDIAKYKKELGAKIYGIEPGNEGNQRILDMINNNK------FSLKGFRLI 172 +G G SY + +Y+ + Y I+ NE N + ++ N+ F G R I Sbjct: 257 IGCGAGAHSYVNGKRYENISNIEKY-IKEINENNSAVEEIHKNSIKDNMEEFMFMGLRKI 315 Query: 173 EASELASF 180 + + F Sbjct: 316 KGICIEDF 323 >gnl|CDD|128367 smart00052, EAL, Putative diguanylate phosphodiesterase. Putative diguanylate phosphodiesterase, present in a variety of bacteria. Length = 241 Score = 26.8 bits (60), Expect = 7.0 Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 6/50 (12%) Query: 41 TTAMTSVILEEI--LGYKTNIKLLAVPV----TFRSLKNKGIDIFMGYWY 84 T I++ I L K ++++A V L++ G D GY + Sbjct: 184 TDPEDEAIVQSIIELAQKLGLQVVAEGVETPEQLDLLRSLGCDYGQGYLF 233 >gnl|CDD|178227 PLN02618, PLN02618, tryptophan synthase, beta chain. Length = 410 Score = 27.0 bits (60), Expect = 7.1 Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 7/50 (14%) Query: 199 EPHPINSDLNIHYLPG-GEEIS---GFGEASVYTVVRSDYLDKCPNISRL 244 EPH I++ L+ PG G E S G A Y+V + L+ +SRL Sbjct: 312 EPHSISAGLD---YPGVGPEHSFLKDTGRAEYYSVTDEEALEAFQRLSRL 358 >gnl|CDD|180213 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated. Length = 424 Score = 26.8 bits (60), Expect = 7.2 Identities = 11/49 (22%), Positives = 22/49 (44%), Gaps = 3/49 (6%) Query: 240 NISRLLKNIKFSVALENEMMKLILNNKQDRQFVGRTMLRTHPDLLKNWL 288 + + LK S + +++KL+L + R+ L +LL N + Sbjct: 165 ELYKRLKRSGLSPEIAEKLLKLLLEHMPPRERTAWRYLL---ELLANMI 210 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.321 0.138 0.405 Gapped Lambda K H 0.267 0.0732 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 5,124,139 Number of extensions: 327776 Number of successful extensions: 658 Number of sequences better than 10.0: 1 Number of HSP's gapped: 656 Number of HSP's successfully gapped: 18 Length of query: 309 Length of database: 5,994,473 Length adjustment: 93 Effective length of query: 216 Effective length of database: 3,984,929 Effective search space: 860744664 Effective search space used: 860744664 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: 57 (25.7 bits)