RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780380|ref|YP_003064793.1| flagellar basal body rod protein FlgC [Candidatus Liberibacter asiaticus str. psy62] (134 letters) >gnl|CDD|31746 COG1558, FlgC, Flagellar basal body rod protein [Cell motility and secretion]. Length = 137 Score = 138 bits (349), Expect = 5e-34 Identities = 59/136 (43%), Positives = 79/136 (58%), Gaps = 7/136 (5%) Query: 4 LIASAHIANSGLAVQSARMQIISENIANARTTGDTPGSDPYRRKTISFEEVMH------G 57 L + +IA S L+ QS R+ +IS NIANA +T G PYRRK + F + G Sbjct: 3 LFSIFNIAGSALSAQSLRLNVISSNIANADSTRTPDG-GPYRRKQVVFSAELFAPTGATG 61 Query: 58 SGGVRVKKIGVDQSTFVEEFDPGHPVANASGIVKYPNVNVLVETADMRETNRLYMANLQT 117 GV+V KI D S F +DPGHP A+A G VK PNVNV++E DM +R Y AN++ Sbjct: 62 GAGVKVSKIVEDPSPFKLVYDPGHPDADAKGYVKMPNVNVVIEMVDMISASRSYEANVEV 121 Query: 118 IKQSHDMMTTTLDLLR 133 + + MM TL+L + Sbjct: 122 LNTAKSMMQKTLELGQ 137 >gnl|CDD|32000 COG1815, FlgB, Flagellar basal body protein [Cell motility and secretion]. Length = 133 Score = 48.4 bits (115), Expect = 6e-07 Identities = 29/138 (21%), Positives = 56/138 (40%), Gaps = 15/138 (10%) Query: 1 MDYLIASAHIANSGLAVQSARMQIISENIANARTTGDTPGSDPYRRKTISFEEVMHGSGG 60 M + + L V+S R ++I+ NIANA DTPG Y+ K + FE V+ + Sbjct: 1 MMSFDRAFGLLQKALDVRSLRQEVIANNIANA----DTPG---YKAKDVDFESVLKKALA 53 Query: 61 VRVKKIGVDQST--FVEEFD----PGHPVANASGIVKYP--NVNVLVETADMRETNRLYM 112 + + +++ + + + + G V++ E + + +Y Sbjct: 54 GNNTTLALAKTSTRHLGPAENIDPTDASLLDRIGDQPNDGNTVDLDREMTEFAKNQLMYQ 113 Query: 113 ANLQTIKQSHDMMTTTLD 130 A L +K M+ + L Sbjct: 114 ALLSFLKSQIKMLNSVLK 131 >gnl|CDD|31935 COG1749, FlgE, Flagellar hook protein FlgE [Cell motility and secretion]. Length = 423 Score = 39.6 bits (92), Expect = 2e-04 Identities = 22/81 (27%), Positives = 33/81 (40%), Gaps = 9/81 (11%) Query: 10 IANSGLAVQSARMQIISENIANARTTGDTPGSDPYRRKTISFEEVMHGS--GGVRVKKIG 67 SG+ + +IS NIANA TTG ++R F ++ S G +G Sbjct: 7 NGVSGMNAHQFALDVISNNIANANTTG-------FKRSRAEFSDMFSQSLVGASTYTALG 59 Query: 68 VDQSTFVEEFDPGHPVANASG 88 V S+ + F G + S Sbjct: 60 VGVSSISQIFTQGSFQSTGSN 80 Score = 31.5 bits (71), Expect = 0.073 Identities = 15/48 (31%), Positives = 26/48 (54%) Query: 86 ASGIVKYPNVNVLVETADMRETNRLYMANLQTIKQSHDMMTTTLDLLR 133 +SG ++ NV++ E ++ R Y AN + I S M+ T ++L R Sbjct: 376 SSGALEMSNVDLAKELTNLIVAQRGYQANAKVITTSDQMLQTLVNLKR 423 >gnl|CDD|34397 COG4786, FlgG, Flagellar basal body rod protein [Cell motility and secretion]. Length = 265 Score = 38.7 bits (90), Expect = 5e-04 Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 7/47 (14%) Query: 9 HIANSGLAVQSARMQIISENIANARTTGDTPGSDPYRRKTISFEEVM 55 + A SG+ Q ++ +IS N+AN TTG ++R FE+++ Sbjct: 6 YTAASGMMAQQRKLDVISNNLANVNTTG-------FKRDRAEFEDLL 45 Score = 32.5 bits (74), Expect = 0.035 Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 11/79 (13%) Query: 64 KKIGVDQSTFVEEFDPGHPVANAS---------GIVKYPNVNVLVETADMRETNRLYMAN 114 KKIG + + E G V G ++ NVNV+ E DM E R Y AN Sbjct: 189 KKIG--NNLYQETAASGPIVGVPGDNGFGAIRQGFLEASNVNVVEEMTDMIEAQRAYEAN 246 Query: 115 LQTIKQSHDMMTTTLDLLR 133 + I+ + +M+ +LLR Sbjct: 247 SKVIQTADEMLGKANNLLR 265 >gnl|CDD|109515 pfam00460, Flg_bb_rod, Flagella basal body rod protein. Length = 31 Score = 33.7 bits (78), Expect = 0.017 Identities = 13/27 (48%), Positives = 16/27 (59%) Query: 10 IANSGLAVQSARMQIISENIANARTTG 36 A S L Q + +I+ NIANA TTG Sbjct: 3 TAVSALNAQQIALDVIANNIANANTTG 29 >gnl|CDD|31448 COG1256, FlgK, Flagellar hook-associated protein [Cell motility and secretion]. Length = 552 Score = 28.8 bits (64), Expect = 0.51 Identities = 17/64 (26%), Positives = 24/64 (37%), Gaps = 14/64 (21%) Query: 10 IANSGLAVQSARMQIISENIANARTTGDTPGSDPYRRKTISFEEV-------MHGSGGVR 62 A SGL A + + NI+NA T G Y R+ + ++ GV Sbjct: 9 TALSGLNAAQAALDVTGHNISNANTPG-------YSRQRVIQTTNIPYLGGGLNVGTGVN 61 Query: 63 VKKI 66 V I Sbjct: 62 VVSI 65 >gnl|CDD|100092 cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and deoxyribose-1-phosphate to the corresponding 5-phosphopentoses. PGM2L1 is thought to catalyze the 1,3-bisphosphoglycerate-dependent synthesis of glucose 1,6-bisphosphate and other aldose-bisphosphates that serve as cofactors for several sugar phosphomutases and possibly also as regulators of glycolytic enzymes. PGM2 and PGM2L1 belong to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.. Length = 487 Score = 27.5 bits (62), Expect = 1.2 Identities = 24/93 (25%), Positives = 33/93 (35%), Gaps = 21/93 (22%) Query: 15 LAVQSARMQIISENIANA---RTTGDTPGSDPYRRKTISFEEV---MHGSGGVRVKKI-- 66 A+ S ++ I E I +A + K + V +HG GG V + Sbjct: 150 EALDSGLIKYIGEEIDDAYLEAVKKLLVNPELNEGKDLKI--VYTPLHGVGGKFVPRALK 207 Query: 67 --GVDQSTFVEE---FDPGHPVANASGIVKYPN 94 G VEE DP P VK+PN Sbjct: 208 EAGFTNVIVVEEQAEPDPDFPT------VKFPN 234 >gnl|CDD|133376 cd04176, Rap2, Rap2 subgroup. The Rap2 subgroup is part of the Rap subfamily of the Ras family. It consists of Rap2a, Rap2b, and Rap2c. Both isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK) are putative effectors of Rap2 in mediating the activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton. In human platelets, Rap2 was shown to interact with the cytoskeleton by binding the actin filaments. In embryonic Xenopus development, Rap2 is necessary for the Wnt/beta-catenin signaling pathway. The Rap2 interacting protein 9 (RPIP9) is highly expressed in human breast carcinomas and correlates with a poor prognosis, suggesting a role for Rap2 in breast cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a, or Rap1b, is expressed in human red blood cells, where it is believed to be involved in vesiculation. A number of additional effector proteins for Rap2 have been identified, including the RalGEFs RalGDS, RGL, and Rlf, which also interact with Rap1 and Ras. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 163 Score = 25.6 bits (56), Expect = 4.2 Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 2/31 (6%) Query: 51 FEEVMHGSGGVRVKKIGVD--QSTFVEEFDP 79 ++ V+ GSGGV + V TF+E++DP Sbjct: 2 YKVVVLGSGGVGKSALTVQFVSGTFIEKYDP 32 >gnl|CDD|133336 cd04136, Rap_like, Rap-like subfamily. The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres. Rap2 is involved in multiple functions, including activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton and activation of the Wnt/beta-catenin signaling pathway in embryonic Xenopus. A number of effector proteins for Rap2 have been identified, including isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK), and the RalGEFs RalGDS, RGL, and Rlf, which also interact with Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and Rap2. In budding yeasts, it is involved in selecting a site for bud growth, which directs the establishment of cell polarization. The Rho family GTPase Cdc42 and its GEF, Cdc24, then establish an axis of polarized growth. It is believed that Cdc42 interacts directly with RSR1 in vivo. In filamentous fungi such as Ashbya gossypii, RSR1 is a key regulator of polar growth in the hypha. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 163 Score = 25.3 bits (56), Expect = 4.7 Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 2/31 (6%) Query: 51 FEEVMHGSGGVRVKKIGVD--QSTFVEEFDP 79 ++ V+ GSGGV + V Q FVE++DP Sbjct: 2 YKVVVLGSGGVGKSALTVQFVQGIFVEKYDP 32 >gnl|CDD|37958 KOG2747, KOG2747, KOG2747, Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]. Length = 396 Score = 25.4 bits (55), Expect = 4.7 Identities = 8/16 (50%), Positives = 11/16 (68%) Query: 39 PGSDPYRRKTISFEEV 54 PG++ YR+ IS EV Sbjct: 187 PGNEIYRKGNISVFEV 202 >gnl|CDD|34398 COG4787, FlgF, Flagellar basal body rod protein [Cell motility and secretion]. Length = 251 Score = 25.3 bits (55), Expect = 5.7 Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 3/36 (8%) Query: 1 MDYLIASAHIANSGLAVQSARMQIISENIANARTTG 36 MD+ I +A A S L Q + + N+ANA TTG Sbjct: 1 MDHAIYTAMGAASQLLEQ---QAVTANNLANASTTG 33 Score = 24.9 bits (54), Expect = 7.1 Identities = 28/119 (23%), Positives = 47/119 (39%), Gaps = 7/119 (5%) Query: 20 ARMQIISENIANARTTGDTPGS----DPYRRKTISFEEVMHGSGGV-RVKKIGVDQSTFV 74 A++ I ++ +A GD + + + +EV G G+ R+ V Sbjct: 133 AKVTIAADGTISALNPGDPANTVAVVGRLKLVQATGQEVQRGDDGLFRLTAETQQPRGQV 192 Query: 75 EEFDPGHPVANASGIVKYPNVNVLVETADMRETNRLYMANLQTIKQSHDMMTTTLDLLR 133 + DP V SG ++ NVN + E DM R + ++ I + D LLR Sbjct: 193 LKADPSVRVM--SGALEGSNVNAVEEMTDMISLARQFEMQMKMISTADDNAGAANQLLR 249 >gnl|CDD|145166 pfam01853, MOZ_SAS, MOZ/SAS family. This region of these proteins has been suggested to be homologous to acetyltransferases. Length = 189 Score = 24.5 bits (54), Expect = 8.3 Identities = 8/16 (50%), Positives = 11/16 (68%) Query: 39 PGSDPYRRKTISFEEV 54 PG++ YR+ IS EV Sbjct: 5 PGNEIYRKGNISVFEV 20 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 0.315 0.130 0.359 Gapped Lambda K H 0.267 0.0747 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,480,540 Number of extensions: 68663 Number of successful extensions: 140 Number of sequences better than 10.0: 1 Number of HSP's gapped: 136 Number of HSP's successfully gapped: 21 Length of query: 134 Length of database: 6,263,737 Length adjustment: 84 Effective length of query: 50 Effective length of database: 4,448,581 Effective search space: 222429050 Effective search space used: 222429050 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 (21.6 bits) S2: 52 (23.8 bits)