RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= 537021.9.peg.816_1
         (97 letters)



>gnl|CDD|163702 cd08071, MPN_DUF2466, Mov34/MPN/PAD-1 family.  Mov34 DUF2466 (also
           known as DNA repair protein RadC) domain of unknown
           function contains the signature JAB1/MPN/Mov34
           metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is
           involved in zinc ion coordination and provides the
           active site for isopeptidase activity. However, to date,
           the name RadC has been misleading and no function has
           been determined.
          Length = 113

 Score =  129 bits (326), Expect = 2e-31
 Identities = 41/92 (44%), Positives = 55/92 (59%)

Query: 1   LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADI 60
           L LD  N LIA E  S GT++   V+ REI +  L  +A +IIL HNHPSG+P PS  DI
Sbjct: 22  LLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDI 81

Query: 61  NMTQNIITTLNPLNIIVHDHIIIGKDAFVSFK 92
            +T+ +      L I + DHII+G   + SF+
Sbjct: 82  ELTKRLKEAGELLGIRLLDHIIVGDGGYFSFR 113


>gnl|CDD|146570 pfam04002, DUF2466, Protein of unknown function (DUF2466).  This
           family was named initially with reference to the E. coli
           radC102 mutation which suggested that RadC was involved
           in repair of DNA lesions. However the relevant mutation
           has subsequently been shown to be in recG, where radC is
           in fact an allele of recG. In addition, a personal
           communication from Claverys, J-P, et al, indicates a
           total failure of all attempts to characterize a
           radiation-related function for RadC in Streptococcus
           pneumoniae, suggesting that it is not involved in repair
           of DNA lesions, in recombination during transformation,
           in gene conversion, nor in mismatch repair.
          Length = 123

 Score =  127 bits (321), Expect = 8e-31
 Identities = 44/92 (47%), Positives = 58/92 (63%)

Query: 1   LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADI 60
           L+LD  N LIA E  S GT++   V+ REI +R L L+A ++IL HNHPSG+P PS ADI
Sbjct: 27  LYLDTQNRLIAVEEVSEGTVNSASVHPREIFKRALRLNAAAVILAHNHPSGDPTPSQADI 86

Query: 61  NMTQNIITTLNPLNIIVHDHIIIGKDAFVSFK 92
            +T+ +      L I + DHIIIG   + SF 
Sbjct: 87  ELTKRLKEAGELLGIRLLDHIIIGDGGYFSFA 118


>gnl|CDD|32186 COG2003, RadC, DNA repair proteins [DNA replication, recombination,
           and repair].
          Length = 224

 Score =  119 bits (301), Expect = 1e-28
 Identities = 41/97 (42%), Positives = 60/97 (61%)

Query: 1   LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADI 60
           L+LD  N LIA E    GT++   V+ REI +  L+ +A ++IL HNHPSG+P PS ADI
Sbjct: 128 LYLDSQNRLIATETLFIGTLNVSEVHPREIFKEALKYNAAAVILAHNHPSGDPTPSRADI 187

Query: 61  NMTQNIITTLNPLNIIVHDHIIIGKDAFVSFKGLRII 97
            +T+ +      L I + DHIIIG+  ++SF    ++
Sbjct: 188 LITERLKEAGKLLGIRLLDHIIIGEGLYISFAERGLL 224


>gnl|CDD|163690 cd08059, MPN_prok_mb, Mpr1p, Pad1p N-terminal (MPN) domains with
          catalytic isopeptidase activity (metal-binding);
          prokaryotic.  This family contains bacterial and
          archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB,
          MPN+)-like domains. These catalytically active domains
          contain the signature JAB1/MPN/Mov34 metalloenzyme
          (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc
          ion coordination and provides the active site for
          isopeptidase activity for the release of ubiquitin from
          ubiquitinated proteins (thus having deubiquitinating
          (DUB) activity) that are tagged for degradation.  The
          JAMM proteins likely hydrolyze ubiquitin conjugates in
          a manner similar to thermolysin, in which the
          zinc-polarized aqua ligand serves as the nucleophile,
          compared with the classical DUBs that do so with a
          cysteine residue in the active site.
          Length = 101

 Score = 37.5 bits (87), Expect = 7e-04
 Identities = 13/29 (44%), Positives = 21/29 (72%)

Query: 35 LELSATSIILVHNHPSGNPNPSDADINMT 63
          LE+    + LVH+HPSG+  PS+AD+++ 
Sbjct: 52 LEIGMKVVGLVHSHPSGSCRPSEADLSLF 80


>gnl|CDD|163703 cd08072, MPN_archaeal, Mov34/MPN/PAD-1 family: archaeal
          JAB1/MPN/Mov34 metalloenzyme.  This family contains
          only archaeal MPN (also known as Mov34, PAD-1, JAMM,
          JAB, MPN+)-like domains. These domains contain the
          signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif,
          EXnHS/THX7SXXD, which is involved in zinc ion
          coordination and provides the active site for
          isopeptidase activity for the release of ubiquitin from
          ubiquitinated proteins (thus having deubiquitinating
          (DUB) activity) that are tagged for degradation.  The
          JAMM proteins likely hydrolyze ubiquitin conjugates in
          a manner similar to thermolysin, in which the
          zinc-polarized aqua ligand serves as the nucleophile,
          compared with the classical DUBs that do so with a
          cysteine residue in the active site.
          Length = 117

 Score = 34.9 bits (81), Expect = 0.005
 Identities = 12/18 (66%), Positives = 16/18 (88%)

Query: 45 VHNHPSGNPNPSDADINM 62
          VH+HPSG+P PSDAD++ 
Sbjct: 65 VHSHPSGSPRPSDADLSF 82


>gnl|CDD|163704 cd08073, MPN_NLPC_P60, Mpr1p, Pad1p N-terminal (MPN) domains with
          catalytic isopeptidase activity (metal-binding) found
          in proteins also containing NlpC/P60 domains.  This
          family contains bacterial MPN (also known as Mov34,
          PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus
          of NlpC/P60 phage tail protein domains. These domains
          contain the signature JAB1/MPN/Mov34 metalloenzyme
          (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc
          ion coordination and provides the active site for
          isopeptidase activity for the release of ubiquitin from
          ubiquitinated proteins (thus having deubiquitinating
          (DUB) activity) that are tagged for degradation.  The
          JAMM proteins likely hydrolyze ubiquitin conjugates in
          a manner similar to thermolysin, in which the
          zinc-polarized aqua ligand serves as the nucleophile,
          compared with the classical DUBs that do so with a
          cysteine residue in the active site.
          Length = 108

 Score = 30.3 bits (69), Expect = 0.12
 Identities = 10/19 (52%), Positives = 14/19 (73%)

Query: 44 LVHNHPSGNPNPSDADINM 62
          +VH+HP G+P PS+AD   
Sbjct: 64 VVHSHPDGSPAPSEADRAQ 82


>gnl|CDD|31501 COG1310, COG1310, Predicted metal-dependent protease of the
          PAD1/JAB1 superfamily [General function prediction
          only].
          Length = 134

 Score = 28.6 bits (63), Expect = 0.38
 Identities = 9/24 (37%), Positives = 15/24 (62%)

Query: 42 IILVHNHPSGNPNPSDADINMTQN 65
          +   H+HP G P PS+AD  +++ 
Sbjct: 72 VGWYHSHPGGPPYPSEADRRLSKL 95


>gnl|CDD|29418 cd00831, CHS_like, Chalcone and stilbene synthases; plant-specific
           polyketide synthases (PKS) and related enzymes, also
           called type III PKSs. PKS generate an array of different
           products, dependent on the nature of the starter
           molecule. They share a common chemical strategy, after
           the starter molecule is loaded onto the active site
           cysteine, a carboxylative condensation reation extends
           the polyketide chain. Plant-specific PKS are dimeric
           iterative PKSs, using coenzyme A esters to deliver
           substrate to the active site, but they differ in the
           choice of starter molecule and the number of
           condensation reactions..
          Length = 361

 Score = 27.9 bits (62), Expect = 0.58
 Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 4/42 (9%)

Query: 19  TIDHVPVYIREIVQRCLE---LSATSI-ILVHNHPSGNPNPS 56
            ++       E  +  L+   L  + I  LV N  +GNP PS
Sbjct: 81  ALEEARELAEEAARGALDEAGLRPSDIDHLVVNTSTGNPTPS 122


>gnl|CDD|99735 cd00610, OAT_like, Acetyl ornithine aminotransferase family. This
           family belongs to pyridoxal phosphate (PLP)-dependent
           aspartate aminotransferase superfamily (fold I). The
           major groups in this CD correspond to ornithine
           aminotransferase, acetylornithine aminotransferase,
           alanine-glyoxylate aminotransferase, dialkylglycine
           decarboxylase, 4-aminobutyrate aminotransferase,
           beta-alanine-pyruvate aminotransferase,
           adenosylmethionine-8-amino-7-oxononanoate
           aminotransferase, and glutamate-1-semialdehyde
           2,1-aminomutase. All the enzymes belonging to this
           family act on basic amino acids and their derivatives
           are involved in transamination or decarboxylation..
          Length = 413

 Score = 27.1 bits (61), Expect = 1.1
 Identities = 10/14 (71%), Positives = 11/14 (78%), Gaps = 1/14 (7%)

Query: 4   DKHNIL-IADEVQS 16
            KH IL IADEVQ+
Sbjct: 222 RKHGILLIADEVQT 235


>gnl|CDD|147423 pfam05218, DUF713, Protein of unknown function (DUF713).  This
           family contains several proteins of unknown function
           from C.elegans. The GO annotation suggests that this
           protein is involved in nematode development and has a
           positive regulation on growth rate.
          Length = 182

 Score = 26.6 bits (59), Expect = 1.6
 Identities = 11/47 (23%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 29  EIVQRCLELSATSIILVHNHPSGNPNPSDADINMTQNIITTLNPLNI 75
           +++Q+ +   AT ++ ++N   G  N S     + Q + + +NP +I
Sbjct: 111 KVLQKSISDQATKLLEIYN-SLGKLNLSKDWYEILQKLFSRINPSSI 156


>gnl|CDD|144240 pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family.  This
           family includes Ribosomal L4/L1 from eukaryotes and
           archaebacteria and L4 from eubacteria. L4 from yeast has
           been shown to bind rRNA.
          Length = 190

 Score = 25.9 bits (58), Expect = 2.4
 Identities = 6/19 (31%), Positives = 11/19 (57%)

Query: 70  LNPLNIIVHDHIIIGKDAF 88
           LN  +++  D ++I K A 
Sbjct: 166 LNVYDLLPADKVVITKSAL 184


>gnl|CDD|30509 COG0160, GabT, 4-aminobutyrate aminotransferase and related
           aminotransferases [Amino acid transport and metabolism].
          Length = 447

 Score = 26.0 bits (57), Expect = 2.6
 Identities = 9/15 (60%), Positives = 11/15 (73%), Gaps = 1/15 (6%)

Query: 3   LDKHNIL-IADEVQS 16
             +H IL IADEVQ+
Sbjct: 252 CREHGILLIADEVQT 266


>gnl|CDD|36656 KOG1443, KOG1443, KOG1443, Predicted integral membrane protein
           [Function unknown].
          Length = 349

 Score = 25.6 bits (56), Expect = 2.9
 Identities = 12/50 (24%), Positives = 22/50 (44%)

Query: 44  LVHNHPSGNPNPSDADINMTQNIITTLNPLNIIVHDHIIIGKDAFVSFKG 93
           L+ N PS   NP D   ++   +   L PL+++     +I   +   F+ 
Sbjct: 186 LLRNQPSAKRNPIDTIFHLQPWMSIGLLPLSLLFEGLHLITSSSIFRFQD 235


>gnl|CDD|32443 COG2262, HflX, GTPases [General function prediction only].
          Length = 411

 Score = 25.6 bits (56), Expect = 3.3
 Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 3/43 (6%)

Query: 4   DKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVH 46
           D   +L+ D V   G I  +P  + E  +  LE    + +L+H
Sbjct: 238 DGRKVLLTDTV---GFIRDLPHPLVEAFKSTLEEVKEADLLLH 277


>gnl|CDD|34597 COG4992, ArgD, Ornithine/acetylornithine aminotransferase [Amino
           acid transport and metabolism].
          Length = 404

 Score = 25.5 bits (56), Expect = 3.6
 Identities = 8/14 (57%), Positives = 10/14 (71%), Gaps = 1/14 (7%)

Query: 4   DKHNIL-IADEVQS 16
           D+H  L I DEVQ+
Sbjct: 215 DEHGALLILDEVQT 228


>gnl|CDD|30851 COG0505, CarA, Carbamoylphosphate synthase small subunit [Amino
           acid transport and metabolism / Nucleotide transport and
           metabolism].
          Length = 368

 Score = 25.2 bits (55), Expect = 3.7
 Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 43  ILVHNHPSGNPNPSDADINMTQNIITTLNPLNIIVHDHIIIG 84
           I + N P G+P P D  I   + ++ T  P+  I   H ++ 
Sbjct: 224 IFLSNGP-GDPAPLDYAIETIKELLGTKIPIFGICLGHQLLA 264


>gnl|CDD|143918 pfam00150, Cellulase, Cellulase (glycosyl hydrolase family 5). 
          Length = 276

 Score = 25.4 bits (56), Expect = 3.7
 Identities = 8/28 (28%), Positives = 13/28 (46%)

Query: 29 EIVQRCLELSATSIILVHNHPSGNPNPS 56
          E+V   ++     II  H+   G+PN  
Sbjct: 69 EVVDAAIDNGMYVIIDWHHDTRGDPNSL 96


>gnl|CDD|143959 pfam00202, Aminotran_3, Aminotransferase class-III. 
          Length = 338

 Score = 25.3 bits (56), Expect = 3.8
 Identities = 9/14 (64%), Positives = 11/14 (78%), Gaps = 1/14 (7%)

Query: 4   DKHNIL-IADEVQS 16
            KH +L IADEVQ+
Sbjct: 208 KKHGVLLIADEVQT 221


>gnl|CDD|163698 cd08067, MPN_2A_DUB, Mov34/MPN/PAD-1 family: Histone H2A
           deubiquitinase.  This family includes histone H2A
           deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM
           and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or
           KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases
           (DUBs), with possible Zn2+-dependent ubiquitin
           isopeptidase activity. It contains the SWIRM (Swi3p,
           Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR,
           TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain
           can bind directly to DNA. 2A-DUB is specific for
           monoubiquitinated H2A (uH2A), regulating transcription
           by coordinating histone acetylation and
           deubiquitination, and destabilizing the association of
           linker histone H1 with nucleosomes. 2A-DUB interacts
           with p/CAF (p300/CBP-associated factor) in a
           co-regulatory protein complex, where the status of
           acetylation of nucleosomal histones modulates its
           deubiquitinase activity. 2A-DUB is a positive regulator
           of androgen receptor (AR) transactivation activity on a
           reporter gene; it participates in transcriptional
           regulation events in androgen receptor-dependent gene
           activation. In prostate tumors, the levels of uH2A are
           dramatically decreased, thus 2A-DUB serving as a
           cancer-related marker.
          Length = 187

 Score = 24.9 bits (55), Expect = 5.0
 Identities = 11/19 (57%), Positives = 14/19 (73%), Gaps = 1/19 (5%)

Query: 46  HNHPSGNPNPSDADINMTQ 64
           H+HP+  PNPS  DI+ TQ
Sbjct: 86  HSHPTFPPNPSLRDID-TQ 103


>gnl|CDD|146859 pfam04427, Brix, Brix domain. 
          Length = 180

 Score = 24.5 bits (54), Expect = 6.3
 Identities = 9/28 (32%), Positives = 16/28 (57%), Gaps = 1/28 (3%)

Query: 27 IREIVQRCLELSATSIILVHNHPSGNPN 54
          ++E+++   E   TS+I+   H  GNP 
Sbjct: 35 LKELLEFAAEKGDTSLIVFGEH-KGNPL 61


>gnl|CDD|163701 cd08070, MPN_like, Mpr1p, Pad1p N-terminal (MPN) domains with
          catalytic isopeptidase activity (metal-binding).  This
          family contains archaeal and bacterial MPN (also known
          as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These
          domains contain the signature JAB1/MPN/Mov34
          metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is
          involved in zinc ion coordination and provides the
          active site for isopeptidase activity for the release
          of ubiquitin from ubiquitinated proteins (thus having
          deubiquitinating (DUB) activity) that are tagged for
          degradation.  The JAMM proteins likely hydrolyze
          ubiquitin conjugates in a manner similar to
          thermolysin, in which the zinc-polarized aqua ligand
          serves as the nucleophile, compared with the classical
          DUBs that do so with a cysteine residue in the active
          site.
          Length = 128

 Score = 24.1 bits (53), Expect = 7.5
 Identities = 7/15 (46%), Positives = 10/15 (66%)

Query: 46 HNHPSGNPNPSDADI 60
          H+HP G   PS+ D+
Sbjct: 77 HSHPDGPARPSETDL 91


>gnl|CDD|163689 cd08058, MPN_euk_mb, Mpr1p, Pad1p N-terminal (MPN) domains with
          catalytic isopeptidase activity (metal-binding);
          eukaryotic.  This family contains eukaryotic MPN (also
          known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found
          in proteins with a variety of functions, including AMSH
          (associated molecule with the Src homology 3 domain
          (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase),
          BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as
          well as Rpn11 (regulatory particle number 11) and CSN5
          (COP9 signalosome complex subunit 5). These domains
          contain the signature JAB1/MPN/Mov34 metalloenzyme
          (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc
          ion coordination and provides the active site for
          isopeptidase activity. Rpn11 is responsible for
          substrate deubiquitination during proteasomal
          degradation. It is essential for maintaining a correct
          cell cycle and normal mitochondrial morphology and
          physiology. CSN5 is critical for nuclear export and the
          degradation of several tumor suppressor proteins,
          including p53, p27, and Smad4. Over-expression of CSN5
          has been implicated in cancer initiation and
          progression. AMSH specifically cleaves Lys 63 and not
          Lys48-linked polyubiquitin (poly-Ub) chains, thus
          facilitating the recycling and subsequent trafficking
          of receptors to the cell surface. It is involved in the
          degradation of EGF receptor (EGFR) and possibly other
          ubiquitinated endocytosed proteins. BRCC36 is part of
          the BRCA1/BRCA2/BARD1-containing nuclear complex that
          displays an E3 ubiquitin ligase activity; it is
          targeted to DNA damage foci after irradiation. 2A-DUB
          is specific for monoubiquitinated H2A (uH2A),
          regulating transcription by coordinating histone
          acetylation and deubiquitination, and destabilizing the
          association of linker histone H1 with nucleosomes. It
          is a positive regulator of androgen receptor (AR)
          transactivation activity on a reporter gene and serves
          as a marker in prostate tumors.
          Length = 119

 Score = 24.1 bits (52), Expect = 8.5
 Identities = 8/19 (42%), Positives = 11/19 (57%), Gaps = 1/19 (5%)

Query: 46 HNHPSGNPNPSDADINMTQ 64
          H+HP+     S  DI+ TQ
Sbjct: 72 HSHPTFTAWLSSVDIH-TQ 89


>gnl|CDD|133056 cd06434, GT2_HAS, Hyaluronan synthases catalyze polymerization of
          hyaluronan.  Hyaluronan synthases (HASs) are
          bi-functional glycosyltransferases that catalyze
          polymerization of hyaluronan. HASs transfer both GlcUA
          and GlcNAc in beta-(1,3) and beta-(1,4) linkages,
          respectively to the hyaluronan chain using UDP-GlcNAc
          and UDP-GlcUA as substrates. HA is made as a free
          glycan, not attached to a protein or lipid. HASs do not
          need a primer for HA synthesis; they initiate HA
          biosynthesis de novo with only UDP-GlcNAc, UDP-GlcUA,
          and Mg2+. Hyaluronan (HA) is a linear
          heteropolysaccharide composed of (1-3)-linked
          beta-D-GlcUA-beta-D-GlcNAc disaccharide repeats. It can
          be found in vertebrates and a few microbes and is
          typically on the cell surface or in the extracellular
          space, but is also found inside mammalian cells.
          Hyaluronan has several physiochemical and biological
          functions such as space filling, lubrication, and
          providing a hydrated matrix through which cells can
          migrate.
          Length = 235

 Score = 24.1 bits (53), Expect = 9.1
 Identities = 8/31 (25%), Positives = 12/31 (38%)

Query: 19 TIDHVPVYIREIVQRCLELSATSIILVHNHP 49
            D  P   RE ++  L      II+V +  
Sbjct: 8  VYDEDPDVFRECLRSILRQKPLEIIVVTDGD 38


>gnl|CDD|36320 KOG1104, KOG1104, KOG1104, Nuclear cap-binding complex, subunit
           NCBP1/CBP80 [RNA processing and modification].
          Length = 759

 Score = 24.1 bits (52), Expect = 9.5
 Identities = 7/15 (46%), Positives = 12/15 (80%)

Query: 24  PVYIREIVQRCLELS 38
           P ++RE++Q+ L LS
Sbjct: 448 PNFVREVIQKELRLS 462


>gnl|CDD|133341 cd04141, Rit_Rin_Ric, Rit/Rin/Ric subfamily.  Rit (Ras-like
          protein in all tissues), Rin (Ras-like protein in
          neurons) and Ric (Ras-related protein which interacts
          with calmodulin) form a subfamily with several unique
          structural and functional characteristics.   These
          proteins all lack a the C-terminal CaaX lipid-binding
          motif typical of Ras family proteins, and Rin and Ric
          contain calmodulin-binding domains.  Rin, which is
          expressed only in neurons, induces neurite outgrowth in
          rat pheochromocytoma cells through its association with
          calmodulin and its activation of endogenous Rac/cdc42. 
          Rit, which is ubiquitously expressed in mammals,
          inhibits growth-factor withdrawl-mediated apoptosis and
          induces neurite extension in pheochromocytoma cells.
          Rit and Rin are both able to form a ternary complex
          with PAR6, a cell polarity-regulating protein, and
          Rac/cdc42.  This ternary complex is proposed to have
          physiological function in processes such as
          tumorigenesis.  Activated Ric is likely to signal in
          parallel with the Ras pathway or stimulate the Ras
          pathway at some upstream point, and binding of
          calmodulin to Ric may negatively regulate Ric activity.
          Length = 172

 Score = 24.0 bits (52), Expect = 9.6
 Identities = 8/26 (30%), Positives = 13/26 (50%)

Query: 2  FLDKHNILIADEVQSRGTIDHVPVYI 27
          F D H+  I D  + +  ID+ P  +
Sbjct: 27 FPDYHDPTIEDAYKQQARIDNEPALL 52


  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
   0.324    0.142    0.413 

Gapped
Lambda     K      H
   0.267   0.0679    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,195,102
Number of extensions: 56022
Number of successful extensions: 174
Number of sequences better than 10.0: 1
Number of HSP's gapped: 174
Number of HSP's successfully gapped: 33
Length of query: 97
Length of database: 6,263,737
Length adjustment: 65
Effective length of query: 32
Effective length of database: 4,859,152
Effective search space: 155492864
Effective search space used: 155492864
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (23.5 bits)