RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780919|ref|YP_003065332.1| dTDP-4-dehydrorhamnose 3,5-epimerase [Candidatus Liberibacter asiaticus str. psy62] (198 letters) >gnl|CDD|144487 pfam00908, dTDP_sugar_isom, dTDP-4-dehydrorhamnose 3,5-epimerase. This family catalyse the isomerisation of dTDP-4-dehydro-6-deoxy -D-glucose with dTDP-4-dehydro-6-deoxy-L-mannose. The EC number of this enzyme is 5.1.3.13. Length = 177 Score = 249 bits (638), Expect = 3e-67 Identities = 88/169 (52%), Positives = 121/169 (71%), Gaps = 1/169 (0%) Query: 6 VRILKTRKFEDSRGWFSQTYSSKLLKELGLQDVFVQDNHSFSFDCGTIRGLHFQRPPYAQ 65 V +++ R F D RG+FS++++++ +E G FVQDNHSFS G +RGLH+Q+PP AQ Sbjct: 9 VLLIEPRVFGDERGFFSESFNAEEFEEAGGHPDFVQDNHSFSSR-GVLRGLHYQQPPPAQ 67 Query: 66 AKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAHGFMTLEMNTEV 125 KLVRC+ G +FD+AVDIR+ SPT+G WV +E+SA N Q++IP GFAHGF+ L + EV Sbjct: 68 GKLVRCVRGEVFDVAVDIRKGSPTFGKWVGVELSAENRRQLWIPEGFAHGFLALSDDAEV 127 Query: 126 IYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLNQ 174 +YKV+ +YS E + G+ W D +I I WPL D PS+SEKD N P L + Sbjct: 128 LYKVSAYYSPEAERGIRWNDPAIGIDWPLADGPEPSLSEKDANAPLLAE 176 >gnl|CDD|32082 COG1898, RfbC, dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes [Cell envelope biogenesis, outer membrane]. Length = 173 Score = 190 bits (485), Expect = 2e-49 Identities = 86/170 (50%), Positives = 116/170 (68%), Gaps = 6/170 (3%) Query: 3 INPVRILKTRKFEDSRGWFSQTYSSKLLKELGLQDVFVQDNHSFSFDCGTIRGLHFQRPP 62 I V I++ + F D RG+F++T+ ++ LGL FVQDNHSFS+ G +RGLH+Q P Sbjct: 8 IPGVLIIEPKVFGDERGFFTETFKAEEFSTLGLPLDFVQDNHSFSYP-GVLRGLHYQHKP 66 Query: 63 YAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAHGFMTLEMN 122 Q KLVR ++G++FD+AVD+R++SPTYG WV + +SA N Q+YIP GFAHGF L + Sbjct: 67 --QGKLVRVVSGKVFDVAVDLRKDSPTYGKWVGVVLSAENKRQLYIPPGFAHGFQVLSDD 124 Query: 123 TEVIYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFL 172 EV+YKVT+ Y EH+ G+ W D +I I WPL D IL S+KD P L Sbjct: 125 AEVVYKVTEEYDPEHERGIPWNDPTIGIDWPLKDPIL---SDKDAAAPLL 171 >gnl|CDD|153388 cd07951, ED_3B_N_AMMECR1, The N-terminal domain, an extradiol dioxygenase class III subunit B-like domain, of unknown proteins containing a C-terminal AMMECR1 domain. This subfamily is composed of uncharacterized proteins containing an N-terminal domain with similarity to the catalytic B subunit of class III extradiol dioxygenases and a C-terminal AMMECR1-like domain. This model represents the N-terminal domain. Class III extradiol dioxygenases use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon, however, proteins in this subfamily do not contain a potential metal binding site and may not exhibit class III extradiol dioxygenase-like activity. The AMMECR1 protein was proposed to be a regulatory factor that is potentially involved in the development of AMME contiguous gene deletion syndrome. Length = 256 Score = 26.9 bits (60), Expect = 3.5 Identities = 13/45 (28%), Positives = 18/45 (40%), Gaps = 1/45 (2%) Query: 27 SKLLKELGLQDVFVQDNHSFSFDCGTIRGLHFQRPPYAQAKLVRC 71 + + GL V D GT+ L+F R + KLVR Sbjct: 91 AGEADKEGL-PVGALGERIPELDHGTLVPLYFLRKAGSDGKLVRI 134 >gnl|CDD|29124 cd02049, bacterial_SERPIN, SERine Proteinase INhibitors (serpins), prokaryotic subgroup. Little information about specific functions is available for this subgroup, most likely they are inhibitory members of the serpin superfamily. In general, serpins exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors.. Length = 364 Score = 26.8 bits (59), Expect = 4.5 Identities = 17/65 (26%), Positives = 24/65 (36%), Gaps = 18/65 (27%) Query: 2 NINPVRILKTRKFEDSRGWFSQ---------------TYSSKL---LKELGLQDVFVQDN 43 N++ +KT E R W Q Y +L LK LG+++ F D Sbjct: 229 NVSLREFVKTLTAEKWRKWIEQFRMREGSLSLPRFQLEYEIELRDALKALGMEEAFTPDA 288 Query: 44 HSFSF 48 FS Sbjct: 289 ADFSK 293 >gnl|CDD|29345 cd00279, YlxR, Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation. Length = 79 Score = 26.4 bits (58), Expect = 5.7 Identities = 8/35 (22%), Positives = 16/35 (45%) Query: 63 YAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLE 97 + +L+R +AG ++ D P G +V + Sbjct: 12 KPKKELIRFVAGPEGEVVPDPTGKLPGRGAYVCAD 46 >gnl|CDD|133356 cd04156, ARLTS1, ARLTS1 subfamily. ARLTS1 (Arf-like tumor suppressor gene 1), also known as Arl11, is a member of the Arf family of small GTPases that is believed to play a major role in apoptotic signaling. ARLTS1 is widely expressed and functions as a tumor suppressor gene in several human cancers. ARLTS1 is a low-penetrance suppressor that accounts for a small percentage of familial melanoma or familial chronic lymphocytic leukemia (CLL). ARLTS1 inactivation seems to occur most frequently through biallelic down-regulation by hypermethylation of the promoter. In breast cancer, ARLTS1 alterations were typically a combination of a hypomorphic polymorphism plus loss of heterozygosity. In a case of thyroid adenoma, ARLTS1 alterations were polymorphism plus promoter hypermethylation. The nonsense polymorphism Trp149Stop occurs with significantly greater frequency in familial cancer cases than in sporadic cancer cases, and the Cys148Arg polymorphism is associated with an increase in high-risk familial breast cancer. Length = 160 Score = 26.2 bits (58), Expect = 5.8 Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 2/33 (6%) Query: 7 RILKTRKFEDSRGWFSQTYSSKLLKELGLQDVF 39 R K +K+ R W+ Q S+ + GL + F Sbjct: 124 RRFKLKKYCSDRDWYVQPCSA--VTGEGLAEAF 154 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 0.323 0.139 0.434 Gapped Lambda K H 0.267 0.0739 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,473,029 Number of extensions: 124588 Number of successful extensions: 210 Number of sequences better than 10.0: 1 Number of HSP's gapped: 206 Number of HSP's successfully gapped: 6 Length of query: 198 Length of database: 6,263,737 Length adjustment: 89 Effective length of query: 109 Effective length of database: 4,340,536 Effective search space: 473118424 Effective search space used: 473118424 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 55 (24.9 bits)