RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780426|ref|YP_003064839.1| hemolysin protein [Candidatus Liberibacter asiaticus str. psy62] (320 letters) >gnl|CDD|132559 TIGR03520, GldE, gliding motility-associated protein GldE. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldC is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. GldE was discovered because of its adjacency to GldD in F. johnsonii. Overexpression of GldE partially supresses the effects of a GldB point mutant suggesting that GldB and GldE interact. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility and in fact some do not appear to express the gliding phenotype. Length = 408 Score = 119 bits (301), Expect = 8e-28 Identities = 67/246 (27%), Positives = 133/246 (54%), Gaps = 17/246 (6%) Query: 71 SETEKEIFNNILRFRKIRIDDIMISRVSINAVEDKATVYEAMLMFEKYGRSWMPVYKNSL 130 ++ E++I I+ F +M R+ I A++ + + E + + G S +PVYK ++ Sbjct: 175 TKEEQKILQGIVSFGNTDTKQVMRPRLDIFALDIETSFSEIIPKIIENGYSRIPVYKETI 234 Query: 131 DNPRGMVHMRDVISYISHMYAKTNNINLNIQLSESNLIKNILFVPSSMLVSDLLTNIQES 190 DN G+++++D++ ++ N N + Q +L++ FVP + + DLL + QE Sbjct: 235 DNITGVLYIKDLLPHL-------NKKNFDWQ----SLLREPYFVPENKKLDDLLRDFQEK 283 Query: 191 RIRMALVIDEHGGTDGLVSYEDIVSVLMRDITSEHHSKKSMISAVSDNTFIVDARTDLEE 250 + +A+V+DE+GGT GLV+ EDI+ ++ DI+ E + + S + DN ++ + +T L++ Sbjct: 284 KNHLAIVVDEYGGTSGLVTLEDIIEEIVGDISDEFDDEDLIYSKIDDNNYVFEGKTSLKD 343 Query: 251 LAKIIGTDCNCL---KGEQDVDSLGGLIFSVLDRIPARGEVVLEIPGFEIVILDADVRCV 307 KI+ + + KGE ++L G + + P +GE + FE I D + + Sbjct: 344 FYKILKLEEDMFDEVKGEA--ETLAGFLLEISGGFPKKGEKIT-FENFEFTIEAMDKKRI 400 Query: 308 RRVRIR 313 ++V++ Sbjct: 401 KQVKVT 406 >gnl|CDD|185050 PRK15094, PRK15094, magnesium/cobalt efflux protein CorC; Provisional. Length = 292 Score = 90.3 bits (224), Expect = 6e-19 Identities = 59/227 (25%), Positives = 119/227 (52%), Gaps = 15/227 (6%) Query: 88 RIDDIMISRVSINAVEDKATVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYIS 147 R+ DIMI R + ++ T+ E + + + S PV D+ G++ +D++ ++ Sbjct: 68 RVRDIMIPRSQMITLKRNQTLDECLDVIIESAHSRFPVISEDKDHIEGILMAKDLLPFM- 126 Query: 148 HMYAKTNNINLNIQLSESNLIKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGL 207 +++ ++ +++ + VP S V +L + R MA+VIDE GG GL Sbjct: 127 ----RSDAEAFSMD----KVLRQAVVVPESKRVDRMLKEFRSQRYHMAIVIDEFGGVSGL 178 Query: 208 VSYEDIVSVLMRDITSEHHSKKSM-ISAVSDNTFIVDARTDLEELAKIIGTDCNCLKGEQ 266 V+ EDI+ +++ +I E+ + + +S +T+ V A +E+ + GT + ++ Sbjct: 179 VTIEDILELIVGEIEDEYDEEDDIDFRQLSRHTWTVRALASIEDFNEAFGTHFS----DE 234 Query: 267 DVDSLGGLIFSVLDRIPARGEVVLEIPGFEIVILDADVRCVRRVRIR 313 +VD++GGL+ +PARGE + +I G++ + AD R + +V ++ Sbjct: 235 EVDTIGGLVMQAFGHLPARGETI-DIDGYQFKVAMADSRRIIQVHVK 280 >gnl|CDD|183209 PRK11573, PRK11573, hypothetical protein; Provisional. Length = 413 Score = 77.5 bits (191), Expect = 5e-15 Identities = 65/241 (26%), Positives = 121/241 (50%), Gaps = 27/241 (11%) Query: 81 ILRFRKIRIDDIMISR---VSINAVED-KATVYEAMLMFEKYGRSWMPVYKNSLDNPRGM 136 +L K+ +DDIM+ R V I+ +D K+ + + L +GR + +Y++SLD+ M Sbjct: 181 VLDLEKVTVDDIMVPRNEIVGIDINDDWKSILRQ--LTHSPHGR--IVLYRDSLDDAISM 236 Query: 137 VHMRDVISYISHMYAKTNNINLNIQLSESNLIK---NILFVPSSMLVSDLLTNIQESRIR 193 + +R+ +Y K + ++ N+++ I FVP +S L Q ++ + Sbjct: 237 LRVRE--AYRLMTEKK--------EFTKENMLRAADEIYFVPEGTPLSTQLVKFQRNKKK 286 Query: 194 MALVIDEHGGTDGLVSYEDIVSVLMRDI-TSEHHSKKSMISAVSDNTFIVDARTDLEELA 252 + LV+DE+G GLV+ EDI+ ++ D TS + ++ +D + I+D ++ E+ Sbjct: 287 VGLVVDEYGDIQGLVTVEDILEEIVGDFTTSMSPTLAEEVTPQNDGSVIIDGTANVREIN 346 Query: 253 KIIGTDCNCLKGEQDVDSLGGLIFSVLDRIPARGEVVLEIPGFEIVILDADVRCVRRVRI 312 K N E D ++ G+I L+ IP G V I ++I ILD +++V++ Sbjct: 347 KAF----NWHLPEDDARTVNGVILEALEEIPVAGTRV-RIGEYDIDILDVQDNMIKQVKV 401 Query: 313 R 313 Sbjct: 402 T 402 >gnl|CDD|162293 TIGR01302, IMP_dehydrog, inosine-5'-monophosphate dehydrogenase. This model describes a rather tightly conserved cluster of IMP dehydrogenase sequences, many of which are characterized. The model excludes two related families of proteins proposed also to be IMP dehydrogenases, but without characterized members. These are related families are the subject of separate models. Length = 450 Score = 34.6 bits (80), Expect = 0.037 Identities = 26/113 (23%), Positives = 53/113 (46%), Gaps = 12/113 (10%) Query: 106 ATVYEAMLMFEKYGRSWMPVYKNSLDNPR--GMVHMRDVISYISHMYAKTNNINLNIQLS 163 TV + + + E+ G S +PV ++ + G++ RD+ + K ++ ++ Sbjct: 97 TTVADVLELMERKGISGIPVVEDGDMTGKLVGIITKRDI------RFVKDKGKPVSEVMT 150 Query: 164 ESNLIKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSV 216 +I VP + + + L + E RI V+D++G GL++ +DIV Sbjct: 151 REEVIT----VPEGIDLEEALKVLHEHRIEKLPVVDKNGELVGLITMKDIVKR 199 >gnl|CDD|180460 PRK06196, PRK06196, oxidoreductase; Provisional. Length = 315 Score = 28.9 bits (65), Expect = 1.6 Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 6/34 (17%) Query: 282 IPARG-----EVVLEIPGFEIVILD-ADVRCVRR 309 +PAR E + I G E+V+LD AD+ VR Sbjct: 55 VPARRPDVAREALAGIDGVEVVMLDLADLESVRA 88 >gnl|CDD|161821 TIGR00331, hrcA, heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene. Length = 337 Score = 28.8 bits (65), Expect = 2.0 Identities = 21/106 (19%), Positives = 42/106 (39%), Gaps = 10/106 (9%) Query: 152 KTNNINLNIQLSESNL--IKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVS 209 K I L +S+ +L NIL +D L S IR ++ + Sbjct: 157 KNKVIELPANISQEDLERAVNIL--------NDRLRGRTLSEIREQIIELLSQLKIEIEE 208 Query: 210 YEDIVSVLMRDITSEHHSKKSMISAVSDNTFIVDARTDLEELAKII 255 +ED + L+ I SE + ++ + S+ + +E + +++ Sbjct: 209 FEDELVDLIISIFSEFNEEELYVDGKSNLLEQPEFFDPIERIRELL 254 >gnl|CDD|128426 smart00116, CBS, Domain in cystathionine beta-synthase and other proteins. Domain present in all 3 forms of cellular life. Present in two copies in inosine monophosphate dehydrogenase, of which one is disordered in the crystal structure [3]. A number of disease states are associated with CBS-containing proteins including homocystinuria, Becker's and Thomsen disease. Length = 49 Score = 28.6 bits (65), Expect = 2.5 Identities = 14/44 (31%), Positives = 22/44 (50%) Query: 174 VPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSVL 217 V + + L ++E IR V+DE G G+V+ DI+ L Sbjct: 5 VSPDTTLEEALELLREHGIRRLPVVDEEGRLVGIVTRRDIIKAL 48 >gnl|CDD|130585 TIGR01522, ATPase-IIA2_Ca, golgi membrane calcium-translocating P-type ATPase. The calcium P-type ATPases have been characterized as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump modelled by TIGR01517. A separate analysis divides Type IIA into sub-types, SERCA and PMR1 the former of which is modelled by TIGR01116. Length = 884 Score = 28.3 bits (63), Expect = 3.0 Identities = 30/130 (23%), Positives = 54/130 (41%), Gaps = 44/130 (33%) Query: 165 SNLIKN--ILFVPSSMLVSDLLTNIQES-RIRMALVIDEHGGTDGLVSYEDIVSVLMRDI 221 S +KN IL + +S ++S + NI ++ I +A++I +V+V Sbjct: 56 SQFVKNPLILLLIASAVISVFMGNIDDAVSITLAILI--------------VVTV---GF 98 Query: 222 TSEHHSKKSMISAVSDNTFIVDARTDLEELAKIIGTDCNCLKGEQDVDSLGG-------L 274 E+ S+KS LE L K++ +C+ ++ + L + Sbjct: 99 VQEYRSEKS-----------------LEALNKLVPPECHLIREGKLEHVLASTLVPGDLV 141 Query: 275 IFSVLDRIPA 284 SV DR+PA Sbjct: 142 CLSVGDRVPA 151 >gnl|CDD|184871 PRK14869, PRK14869, putative manganese-dependent inorganic pyrophosphatase; Provisional. Length = 546 Score = 28.3 bits (64), Expect = 3.2 Identities = 22/93 (23%), Positives = 37/93 (39%), Gaps = 4/93 (4%) Query: 167 LIKNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSVLMR----DIT 222 I + V + + + E+ ++ V+DE G GLVS D+ M +I Sbjct: 74 EIDKPVTVSPDTSLKEAWNLMDENNVKTLPVVDEEGKLLGLVSLSDLARAYMDILDPEIL 133 Query: 223 SEHHSKKSMISAVSDNTFIVDARTDLEELAKII 255 S+ + I D +V A D E K++ Sbjct: 134 SKSPTSLENIIRTLDGEVLVGAEEDKVEEGKVV 166 >gnl|CDD|177609 PHA03372, PHA03372, DNA packaging terminase subunit 1; Provisional. Length = 668 Score = 27.8 bits (62), Expect = 3.5 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 10/72 (13%) Query: 79 NNILRFRKIRIDDIMISRVSINAVEDKATVYEAMLMFEKYGRSW--MPVYKNSLDNPRGM 136 N +L + D +S S+N + KATV+ L+ ++G++W +P+ L N G+ Sbjct: 177 NRVLEYLLHVFDIEFLSESSLNIFKQKATVF---LVPRRHGKTWFIIPIISFLLKNIIGI 233 Query: 137 VHMRDVISYISH 148 I Y++H Sbjct: 234 -----SIGYVAH 240 >gnl|CDD|105955 PRK12820, PRK12820, bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional. Length = 706 Score = 27.6 bits (61), Expect = 4.6 Identities = 22/73 (30%), Positives = 31/73 (42%), Gaps = 6/73 (8%) Query: 64 ASLEGIFSETEKEIFNNILRFRKIRIDDIMIS----RVSINAVEDKATVYEAMLMFEKYG 119 A IF T IF IL+ R RI I I ++S N ++++ E F G Sbjct: 311 ADATDIFENTRYGIFKQILQ-RGGRIKGINIKGQSEKLSKNVLQNE-YAKEIAPSFGAKG 368 Query: 120 RSWMPVYKNSLDN 132 +WM LD+ Sbjct: 369 MTWMRAEAGGLDS 381 >gnl|CDD|162590 TIGR01899, cas_TM1807_csm5, CRISPR-associated RAMP protein, Csm5 family. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. Members of this cas gene family are found in the mtube subtype of CRISPR/cas locus and designated Csm5, for CRISPR/cas Subtype Mtube, protein 5. Length = 365 Score = 26.7 bits (59), Expect = 7.7 Identities = 19/113 (16%), Positives = 31/113 (27%), Gaps = 10/113 (8%) Query: 56 GIRLPRIDASLEGIFSETEKEIFNNILRFRKIRIDDIMISRVSINAVEDKATVYEAMLMF 115 G R + GI + K+ N++ R +++ D R V Y Sbjct: 152 GRAFERKELKKNGISNTIPKDPVNDVFRA--LKVSDSRPLRTDRLIVHRIKLNY------ 203 Query: 116 EKYGRSWMPVYKNSLDNPRGMVHMRDVISYISHMYAKTNNINLNIQLSESNLI 168 GR +P+Y LD + E+ L Sbjct: 204 --NGRPGIPLYAECLDPGTTFSFNVKIDREELKRGLDRKKQFYAPSEGENKLE 254 >gnl|CDD|114953 pfam06261, LktC, Actinobacillus actinomycetemcomitans leukotoxin activator LktC. This family consists of several Actinobacillus actinomycetemcomitans leukotoxin activator (LktC) proteins. Actinobacillus actinomycetemcomitans is a Gram-negative bacterium that has been implicated in the etiology of several forms of periodontitis, especially localized juvenile periodontitis. LktC along with LktB and LktD are thought to be required for activation and localisation of the leukotoxin. Length = 150 Score = 26.6 bits (58), Expect = 8.4 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 6/53 (11%) Query: 26 ISKTSVPAFWTRTIR------ALCKTWKLMKLSHHKGIRLPRIDASLEGIFSE 72 +S T F+ R I+ LC+ WKL++ K ++ I A + GIF E Sbjct: 1 MSGTEYAPFYLRFIQFPNNEVLLCEYWKLVQNFVKKIRKITVIFAQIIGIFGE 53 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 0.136 0.389 Gapped Lambda K H 0.267 0.0710 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 5,172,867 Number of extensions: 330879 Number of successful extensions: 647 Number of sequences better than 10.0: 1 Number of HSP's gapped: 637 Number of HSP's successfully gapped: 24 Length of query: 320 Length of database: 5,994,473 Length adjustment: 93 Effective length of query: 227 Effective length of database: 3,984,929 Effective search space: 904578883 Effective search space used: 904578883 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 (21.9 bits) S2: 57 (25.8 bits)