RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780224|ref|YP_003064637.1| hypothetical protein CLIBASIA_00545 [Candidatus Liberibacter asiaticus str. psy62] (382 letters) >gnl|CDD|34910 COG5330, COG5330, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 364 Score = 125 bits (316), Expect = 2e-29 Identities = 87/320 (27%), Positives = 139/320 (43%), Gaps = 1/320 (0%) Query: 1 MSVQSFIKWAKNAKLQERISIARILGRTWCMEELLDQEKDSLVLAMMHLLDDPSSRVRLS 60 + Q I+ + A ER AR+L L ++ LLDD S VR Sbjct: 7 STDQDLIRLLEEASSGERALAARVLAFASLQRPLSREDMRQFEDLARPLLDDSSEEVRRE 66 Query: 61 LARAIALSDTAPKHVVLALSEDHPDVSGTIILHSPVLKDNDLVDLIGRGNKLTSIFVASR 120 LA A+A +TAP+ + AL+ED ++ +++ SP L D+DLVD+ R + +A R Sbjct: 67 LAAALAQCETAPRALARALAEDPISIAAPLLIRSPALTDDDLVDIARRQGPAHARAIARR 126 Query: 121 HKLSHVVVENLIETGCVDNIVALLGNKSVFLSNSLLMQIVERFCHDASIRNLLSLRTDLS 180 LS +V++ L+E G + ++ LL N + LS L ++ +R + ++R R L Sbjct: 127 PSLSPLVIDALVERGDEEEVLVLLENDAAPLSPYALQRVADRAAAEPALRQAAVDREALP 186 Query: 181 LKARYLLMKSVCNVLSQSKIVQKSITFRRTQILFEESMRVGILEMISHVRDVQALRELVD 240 L+AR L V L S +V+ I+ R L + R + + V Sbjct: 187 LRARIELAARVGERLRDSILVKAQISEARAAELVRFA-RERAAILFAAALADALDIRFVA 245 Query: 241 LLHDDGQLTPALLIYAIMIGAIDFVSVILANIAEYSTDRVYSILSTGGFHVICALYELVG 300 L L+PALL A+ + F L ++A + RV I G H + A+ Sbjct: 246 ALRIMLSLSPALLAAALRSLGLSFFEAALVDLAGLPSHRVRRIGRGGRPHALRAILRTAA 305 Query: 301 LSPEISEIFVEATMIWRELA 320 L + F + R+ A Sbjct: 306 LDERVRSWFRADALELRDHA 325 >gnl|CDD|33613 COG3820, COG3820, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 230 Score = 32.0 bits (72), Expect = 0.27 Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 3/59 (5%) Query: 52 DPSSRVRLSLARAIALSDT---APKHVVLALSEDHPDVSGTIILHSPVLKDNDLVDLIG 107 DP+ R+++ + + L ++ P++ ++ +D PD ++ + P LKD + LIG Sbjct: 71 DPNYRLKILSSPKVELPESKKKGPRYTPVSRRQDRPDAILWLLRNHPELKDAQISKLIG 129 >gnl|CDD|31162 COG0820, COG0820, Predicted Fe-S-cluster redox enzyme [General function prediction only]. Length = 349 Score = 29.9 bits (67), Expect = 1.2 Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 3/54 (5%) Query: 62 ARAIALSDTAPKHVVLALSEDHPDVSGTIILHSPVLKDNDLVDLIGRGNKLTSI 115 R I +S + + L+++ V+ I LH+P +++L D + NK I Sbjct: 188 KRRITVSTSGIVPRIRKLADEQLGVALAISLHAP---NDELRDQLMPINKKYPI 238 >gnl|CDD|34181 COG4533, COG4533, ABC-type uncharacterized transport system, periplasmic component [General function prediction only]. Length = 564 Score = 29.5 bits (66), Expect = 1.5 Identities = 11/42 (26%), Positives = 18/42 (42%) Query: 106 IGRGNKLTSIFVASRHKLSHVVVENLIETGCVDNIVALLGNK 147 GRG + F+ + L + E L+E G + + LL Sbjct: 59 AGRGKRSRLTFLRTPEALLLQLAEKLLEQGKIGQALQLLQLD 100 >gnl|CDD|32412 COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]. Length = 215 Score = 27.9 bits (62), Expect = 4.3 Identities = 22/98 (22%), Positives = 36/98 (36%), Gaps = 20/98 (20%) Query: 232 VQALRELVDLLHDDGQLTPALLIYAIMIGAI-------DFVSVILANIAEY--------- 275 + +EL+ L D G PA I+IGAI V L N+ Sbjct: 9 TKIYKELLRLYGDQGWW-PADNKDEIIIGAILTQNTSWKNVEKALENLKNEGILNLKKIL 67 Query: 276 --STDRVYSILSTGGFHVICALYELVGLSPEISEIFVE 311 + + ++ GF+ A L LS +++ F+ Sbjct: 68 KLDEEELAELIRPSGFYNQKAKR-LKALSKNLAKFFIN 104 >gnl|CDD|34260 COG4641, COG4641, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 373 Score = 28.0 bits (62), Expect = 4.8 Identities = 21/93 (22%), Positives = 34/93 (36%), Gaps = 4/93 (4%) Query: 277 TDRVYSILSTGGFHVICALYELVGLSPEISEIFVE---ATMIWRELAVGSTVMEPGIIAE 333 T+RV+ I GGF + +L +I V + + + + E IAE Sbjct: 277 TNRVFEIAGCGGFLITDYWKDLEKFFKPGKDIIVYQDSKDLKEKLKYLLNHPDERKEIAE 336 Query: 334 KLLERMRKRNISGLPAGELLEMVERIYLDVNRR 366 ER+ R+ +LL + I R Sbjct: 337 CAYERVLARHTYEERIFKLLNEIASI-NIRAGR 368 >gnl|CDD|48074 cd01972, Nitrogenase_VnfE_like, Nitrogenase_VnfE_like: VnfE subunit of the VnfEN complex_like. This group in addition to VnfE contains a subset of the alpha subunit of the nitrogenase MoFe protein and NifE-like proteins. The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of MoFe protein of the molybdenum(Mo)-nitrogenase. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to NifEN where it is further processed to FeMoco. VnfEN may similarly be a scaffolding protein for the iron-vanadium cofactor (FeVco) of the vanadium-dependent (V)-nitrogenase. NifE and NifN are essential for the Mo-nitrogenase, VnfE and VnfN are not essential for the V-nitrogenase. NifE and NifN can substitute when the vnfEN genes are inactivated.. Length = 426 Score = 27.6 bits (61), Expect = 6.1 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 8/82 (9%) Query: 21 IARILGRTWCMEELLDQEKDSLVLAMMHLLDDPSSRVRLSLARAIALSDTAPKHVVLA-- 78 IA++LG E ++++E + V + L R L +AI + A H+++A Sbjct: 259 IAKVLGMEAEAEAVIEREHE-RVAPEIEEL-----RKALKGKKAIVETGAAYGHLLIAVL 312 Query: 79 LSEDHPDVSGTIILHSPVLKDN 100 +V ++ H D Sbjct: 313 RELGFGEVPVVLVFHHDPTYDR 334 >gnl|CDD|176202 cd08240, 6_hydroxyhexanoate_dh_like, 6-hydroxyhexanoate dehydrogenase. 6-hydroxyhexanoate dehydrogenase, an enzyme of the zinc-dependent alcohol dehydrogenase-like family of medium chain dehydrogenases/reductases catalyzes the conversion of 6-hydroxyhexanoate and NAD(+) to 6-oxohexanoate + NADH and H+. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains, at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. Length = 350 Score = 27.2 bits (61), Expect = 7.0 Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 6/37 (16%) Query: 260 GAIDFVSVILANIAEYSTDRVYSILSTGGFHVICALY 296 IDFV+ + + IL+ GG V+ L+ Sbjct: 246 AVIDFVN------NSATASLAFDILAKGGKLVLVGLF 276 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.324 0.137 0.379 Gapped Lambda K H 0.267 0.0714 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,365,316 Number of extensions: 235350 Number of successful extensions: 884 Number of sequences better than 10.0: 1 Number of HSP's gapped: 882 Number of HSP's successfully gapped: 25 Length of query: 382 Length of database: 6,263,737 Length adjustment: 96 Effective length of query: 286 Effective length of database: 4,189,273 Effective search space: 1198132078 Effective search space used: 1198132078 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 58 (26.1 bits)