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)