RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|255764478|ref|YP_003065205.2| aminopeptidase protein [Candidatus Liberibacter asiaticus str. psy62] (418 letters) >gnl|CDD|145308 pfam02073, Peptidase_M29, Thermophilic metalloprotease (M29). Length = 404 Score = 494 bits (1275), Expect = e-140 Identities = 171/401 (42%), Positives = 250/401 (62%), Gaps = 2/401 (0%) Query: 16 LEKLAKVALQVGVNIQEGQHLIVMAPVSALPLARLITKHAYMLGAGLVSVFYKDSEATLM 75 LEK A++ ++VGVN+Q+GQ +++ APV A PL R + + AY GA V V + D E T Sbjct: 6 LEKYAELLVKVGVNVQKGQTVLISAPVEAAPLVRALVEEAYEAGAKNVVVEWSDDEITRA 65 Query: 76 LYKYGADYAFDRVADWFCEGLAKAYSDNTALLSISGDNPLLLVNEDSDKVSRVNQAYLKA 135 ++ + F+ +W EG+ + + A +SI G+NP LL + D ++++ +A A Sbjct: 66 RLEHAPEEQFEEFPEWEAEGMLELAEEGDAFISIRGENPDLLADVDPERIAAYQKARGPA 125 Query: 136 YKPALERISNFDINWSIVPFPSCAWAEIVYPDDPVPIAIAKLANTIFSVSRAHCIDPIAA 195 KP + ++W +V +P+ AWA+ V+P + A+ L + IF R DP+AA Sbjct: 126 LKPRRSATMSNKVSWCVVAYPTPAWAQKVFPQAGM--AVEALWDFIFKAVRLDEEDPVAA 183 Query: 196 WAEHNNFLHQKSQWLSQRDFAEIRFSGPNTSLKVGLAEGHRWSGGSSIAQNGIMCNPNIP 255 W H+ L +K L+++ F ++ + P T L V L H W+GG S ++G+ N+P Sbjct: 184 WEAHDEKLKKKVDILNEKRFKKLHYKAPGTDLTVSLPGRHAWNGGGSKNKDGVEFIANMP 243 Query: 256 TEEVFTAPHARRVEGYATSTKPLVYQGMLIENIRVRFDQGRVVEASASKGEEMLNKILDI 315 TEEVFTAP VEG TSTKPL YQG LIE IR+ F+ G+VV+ASA KGEE+L K+LD Sbjct: 244 TEEVFTAPVKDSVEGTVTSTKPLSYQGNLIEGIRLTFEDGKVVDASAEKGEEVLKKLLDT 303 Query: 316 DEGARRLGEVALVPHSSLLSKMNTLFYDTLFDENAASHIAFGQCYSKCFKKPDNALDNWL 375 DEGAR LGEVALVP+ S +S + +FY+TLFDENA+ H+A G+ Y +C + D L Sbjct: 304 DEGARYLGEVALVPNPSPISNIGIIFYNTLFDENASCHLALGRAYPECIEGGKEMSDEEL 363 Query: 376 EERGGNSSITHIDWMIGSGDMNVDGLTKNGVLVPIMRGGEW 416 + GGN S H+D+MIGSG++++DG+TK+G PI R G + Sbjct: 364 KAGGGNDSAVHVDFMIGSGEIDIDGITKDGTREPIFRNGNF 404 >gnl|CDD|32463 COG2309, AmpS, Leucyl aminopeptidase (aminopeptidase T) [Amino acid transport and metabolism]. Length = 385 Score = 355 bits (913), Expect = 1e-98 Identities = 162/405 (40%), Positives = 227/405 (56%), Gaps = 26/405 (6%) Query: 16 LEKLAKVALQVGVNIQEGQHLIVMAPVSALPLARLITKHAYMLGAGLVSVFYKDSEATLM 75 LEK A++ ++VG+N+Q GQ +++ APV ALPL RLI K AY GA V V D E Sbjct: 4 LEKYAELLVKVGINLQPGQKVVISAPVDALPLVRLIVKEAYEAGARPVKVCLGDPEVARA 63 Query: 76 LYKYGADYAFDRVADWFCEGLAKAYSDNTALLSISGDNPLLLVNEDSDKVSRVNQAYLKA 135 +Y D F+ + +W + +A ++ A L I+ + LL ED KV+ +A KA Sbjct: 64 VYTLAPDEEFEEIPEWEAAAMEEADANGAARLPINTEG--LLDEEDPAKVAAAQKAGAKA 121 Query: 136 YKPALERISNFDINWSIVPFPSCAWAEIVYPDDPVPIAIAKLANTIFSVSRAHCIDPIAA 195 KP IS+ ++W++V +P+ +WA+ V+P+ A+AKL + IF R Sbjct: 122 VKPVRISISSNKVSWTVVRYPAPSWAKRVFPE-----AVAKLEDFIFRAVRVD------E 170 Query: 196 WAEHNNFLHQKSQWLSQRDFAEIRFSGPN-TSLKVGLAEGHRWSGGSSIAQNGIMCNPNI 254 W EH+ L + ++ L++ + + P T L GLA H W+ S+ + G N N+ Sbjct: 171 WEEHSALLEKLAEILNEAS--AVHITTPGGTDLTFGLAGRHAWNDAGSVNKGG---NANM 225 Query: 255 PTEEVFTAPHARRVEGYATSTKPLVYQGMLIENIRVRFDQGRVVEASASKGEEMLNKILD 314 PT EVFTAPH V G KPL YQG LIE IR+ F+ G+VVE SA KGEE+L ++LD Sbjct: 226 PTGEVFTAPHEDSVNGVVVFDKPLSYQGTLIEGIRLTFEDGKVVEISAEKGEEVLKRLLD 285 Query: 315 IDEGARRLGEVALVPHSSLLSKMNTLFYDTLFDENAAS--HIAFGQCYSKCFKKPDNALD 372 DEGARRLGE+AL P S + LFY+ LFDE A+ HIA G Y + + Sbjct: 286 TDEGARRLGELALGP----NSPIARLFYNILFDEKASGTVHIAIGSAYPFNVEG-GAEMQ 340 Query: 373 NWLEERGGNSSITHIDWMIGSGDMNVDGLTKNGVLVPIMRGGEWA 417 N G N S H+D MIGS ++ +DG+ +G P+ R GEWA Sbjct: 341 NESAIHGDNVSDVHVDSMIGSSEVYIDGVLVDGNGEPVFRKGEWA 385 >gnl|CDD|35304 KOG0081, KOG0081, KOG0081, GTPase Rab27, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]. Length = 219 Score = 30.0 bits (67), Expect = 1.3 Identities = 10/42 (23%), Positives = 23/42 (54%) Query: 62 LVSVFYKDSEATLMLYKYGADYAFDRVADWFCEGLAKAYSDN 103 L + F++D+ L+++ ++ +F V +W + AY +N Sbjct: 83 LTTAFFRDAMGFLLIFDLTSEQSFLNVRNWLSQLQTHAYCEN 124 >gnl|CDD|35519 KOG0298, KOG0298, KOG0298, DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]. Length = 1394 Score = 29.2 bits (65), Expect = 2.2 Identities = 26/115 (22%), Positives = 48/115 (41%), Gaps = 20/115 (17%) Query: 208 QWLSQRDFAEIRFSGPNTSLKVGLAEGHRWSGGSSIAQ----NGIMCNPNIPTEEV---- 259 QW EI + LKV L G R + S + + ++ +I E+ Sbjct: 434 QWFE-----EIHKHIS-SLLKVLLYFGIRKTFWLSPFELLQYDIVLTTYDILRNELYHTE 487 Query: 260 -FTAPHARRVEG-YATSTKPLVYQGMLIENIRVRFDQGRVVEASASKGEEMLNKI 312 F + R + Y PL +++ R+ D+ ++VE+S+S EM+ ++ Sbjct: 488 DFGSDRQLRHQSRYMRPNSPL----LMVNWWRICLDEAQMVESSSSAAAEMVRRL 538 >gnl|CDD|133327 cd04127, Rab27A, Rab27a subfamily. The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated insulin secretion, making it a potential target for diabetes therapy. When bound to JFC1 in prostate cells, Rab27a is believed to regulate the exocytosis of prostate- specific markers. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 180 Score = 28.6 bits (64), Expect = 3.5 Identities = 10/42 (23%), Positives = 22/42 (52%) Query: 62 LVSVFYKDSEATLMLYKYGADYAFDRVADWFCEGLAKAYSDN 103 L + F++D+ L+++ + +F V +W + AY +N Sbjct: 79 LTTAFFRDAMGFLLIFDLTNEQSFLNVRNWMSQLQTHAYCEN 120 >gnl|CDD|147061 pfam04710, Pellino, Pellino. Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase. Length = 416 Score = 28.2 bits (63), Expect = 4.0 Identities = 15/26 (57%), Positives = 16/26 (61%), Gaps = 2/26 (7%) Query: 389 WMIGSGDMNVDGLTKNGVLVPIMRGG 414 W G+M DGLT NGVLV RGG Sbjct: 171 WQNPDGEM--DGLTTNGVLVMHPRGG 194 >gnl|CDD|35306 KOG0083, KOG0083, KOG0083, GTPase Rab26/Rab37, small G protein superfamily [General function prediction only]. Length = 192 Score = 28.1 bits (62), Expect = 4.4 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 2/47 (4%) Query: 66 FYKDSEATLMLYKYGADYAFDRVADWFCEGLAKAYSDNTALLSISGD 112 +Y+D++A L+LY +FD W E Y+ L + G+ Sbjct: 67 YYRDADALLLLYDIANKASFDNCQAWLSE--IHEYAKEAVALMLLGN 111 >gnl|CDD|145189 pfam01888, CbiD, CbiD. CbiD is essential for cobalamin biosynthesis in both S. typhimurium and B. megaterium, no functional role has been ascribed to the protein. The CbiD protein has a putative S-AdoMet binding site. It is possible that CbiD might have the same role as CobF in undertaking the C-1 methylation and deacylation reactions required during the ring contraction process. Length = 261 Score = 27.8 bits (62), Expect = 5.6 Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 6/52 (11%) Query: 283 MLIENIR--VRFDQGRVVEASASKGEEM----LNKILDIDEGARRLGEVALV 328 M+ EN++ +R D+G +V S +GEE+ LN L I G LG +V Sbjct: 123 MIRENLQKALREDEGVMVTISVPEGEELAKKTLNARLGIVGGISILGTTGIV 174 >gnl|CDD|31221 COG1018, Hmp, Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]. Length = 266 Score = 27.6 bits (61), Expect = 6.8 Identities = 9/33 (27%), Positives = 14/33 (42%) Query: 29 NIQEGQHLIVMAPVSALPLARLITKHAYMLGAG 61 +++ G L V AP L L + +L G Sbjct: 87 HLKVGDTLEVSAPAGDFVLDDLPERKLLLLAGG 119 >gnl|CDD|99847 cd06144, REX4_like, DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherchia coli RNase T. Length = 152 Score = 27.5 bits (62), Expect = 7.4 Identities = 12/20 (60%), Positives = 16/20 (80%), Gaps = 2/20 (10%) Query: 16 LEKLAKVALQVGVNIQEGQH 35 L+KLAK L G++IQEG+H Sbjct: 121 LKKLAKQLL--GLDIQEGEH 138 >gnl|CDD|132926 cd07015, Clp_protease_NfeD, Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cleaving hydrophobic substrates. Difference in oligomeric form and catalytic residues between 1510-N (forming a dimer) and ClpP (forming a tetradecamer) shows a possible functional difference: 1510-N is likely to have a regulatory function while ClpP is involved in protein quality control. Length = 172 Score = 27.4 bits (60), Expect = 8.1 Identities = 12/29 (41%), Positives = 15/29 (51%) Query: 23 ALQVGVNIQEGQHLIVMAPVSALPLARLI 51 A G I G HLI MAP +++ R I Sbjct: 72 AASAGTYIALGSHLIAMAPGTSIGACRPI 100 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 0.319 0.134 0.407 Gapped Lambda K H 0.267 0.0640 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,110,283 Number of extensions: 269024 Number of successful extensions: 567 Number of sequences better than 10.0: 1 Number of HSP's gapped: 560 Number of HSP's successfully gapped: 14 Length of query: 418 Length of database: 6,263,737 Length adjustment: 96 Effective length of query: 322 Effective length of database: 4,189,273 Effective search space: 1348945906 Effective search space used: 1348945906 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: 59 (26.7 bits)