RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy10277
         (305 letters)



>gnl|CDD|216912 pfam02167, Cytochrom_C1, Cytochrome C1 family. 
          Length = 217

 Score =  324 bits (832), Expect = e-112
 Identities = 124/231 (53%), Positives = 147/231 (63%), Gaps = 22/231 (9%)

Query: 37  WSHSGLLDSFDHASIRRGYEVYKNVCAACHSARFICYRNLVGVSHTEAEAKREAEEIMVE 96
           WS +G   SFD AS++RG +VY  VCAACHS +++ YR L  +  TE E K  A E  V+
Sbjct: 1   WSFAGPFGSFDKASLQRGAQVYTEVCAACHSLKYVRYRRLADLGLTEDEVKANAAEYEVK 60

Query: 97  DGPNEKGEMFKRPGKLSDTFPSPYPNEEAARAANNGAYPPDLSYITMARHGAEDYVFHLL 156
           DGP+  GEMF+RPGK  DTFPSPYPNEEAAR ANNGA PPDLS I  ARHG  DY++ LL
Sbjct: 61  DGPDT-GEMFERPGKPGDTFPSPYPNEEAARWANNGAAPPDLSLIAKARHGGPDYIYSLL 119

Query: 157 TGYMDPPAGDYVFHLLTGYMDPPAGVQIREGLYFNPYFLGGAIGMAQALYNEIIEYEDGT 216
           TGY D PA                 V++R G Y+NPYF GGAI M   L +  +EYEDGT
Sbjct: 120 TGYYDDPA-----------------VELRPGGYYNPYFPGGAIAMPPPLSDGQVEYEDGT 162

Query: 217 PATQSQLAKDVSTFLKWCGEPEHDTRKRMAIKCMTTLGVLAGGAGALLYAL 267
           PAT  Q+AKDV  FL W  EPE D RKR+ +K +  L +L      LLY L
Sbjct: 163 PATYDQMAKDVVAFLMWAAEPELDERKRLGLKVLLFLLILTV----LLYLL 209


>gnl|CDD|225413 COG2857, CYT1, Cytochrome c1 [Energy production and conversion].
          Length = 250

 Score =  199 bits (507), Expect = 5e-63
 Identities = 94/246 (38%), Positives = 119/246 (48%), Gaps = 22/246 (8%)

Query: 24  QAGDLELHPPHLKWSHSGLLDSFDHASIRRGYEVYKNVCAACHSARFICYRNLVGVSHTE 83
            A   EL      W   G  D FD  S++RG ++YK  C+ACHS +   YR L  +   +
Sbjct: 16  AAPFKELAHGKEVWLFKGPFDLFDKGSLQRGAQLYKEYCSACHSLKLQRYRRLKDLGLPD 75

Query: 84  AEAKREAEEIMVEDGPNEKGEMFKRPGKLSDTFPSPYPNEEAARAANNGAYPPDLSYITM 143
            E K  A E  VED P + G MF RP   +D F +P P+   A  AN GA P DL     
Sbjct: 76  DE-KFLALEFTVEDKPGDTGHMFMRPADAADWFGAPPPDLTLAARANGGAAPYDLLRQFY 134

Query: 144 AR-HGAEDYVFHLLTGYMDPPAGDYVFHLLTGYMDPPAGVQIREGLYFNPYFLGG-AIGM 201
           AR HG  DY+  LLTGY+D                PPAG++  +G  +NPYF G   I +
Sbjct: 135 ARCHGVPDYINSLLTGYVDL---------------PPAGLRTPQGTSYNPYFEGELGIFI 179

Query: 202 AQALYNEIIEYEDGTPATQSQLAKDVSTFLKWCGEPEHDTRKRMAIKCMTTLGVLAGGAG 261
           A  L ++   Y  G PA   Q  KD+  +LKW  EPE + RKR+  K M  L V      
Sbjct: 180 ADPLKDKPGTYMPGNPALTDQEVKDLVAYLKWAAEPEKEERKRLGFKVMIFLVVFTI--- 236

Query: 262 ALLYAL 267
            L Y L
Sbjct: 237 -LAYLL 241


>gnl|CDD|205620 pfam13442, Cytochrome_CBB3, Cytochrome C oxidase, cbb3-type,
          subunit III. 
          Length = 67

 Score = 32.0 bits (73), Expect = 0.044
 Identities = 8/20 (40%), Positives = 9/20 (45%)

Query: 49 ASIRRGYEVYKNVCAACHSA 68
          A    G  +Y   CAACH  
Sbjct: 1  ADAAAGEALYDANCAACHGT 20


>gnl|CDD|215669 pfam00034, Cytochrom_C, Cytochrome c.  The Pfam entry does not
          include all Prosite members. The cytochrome 556 and
          cytochrome c' families are not included. All these are
          now in a new clan together. The C-terminus of DUF989,
          pfam06181, has now been merged into this family.
          Length = 81

 Score = 30.6 bits (69), Expect = 0.19
 Identities = 7/16 (43%), Positives = 11/16 (68%)

Query: 53 RGYEVYKNVCAACHSA 68
          +G +++   CAACH A
Sbjct: 1  KGKKLFAANCAACHGA 16


>gnl|CDD|200515 cd11254, Sema_3F, The Sema domain, a protein interacting module, of
           semaphorin 3F (Sema3F).  Sema3F is coexpressed with
           semaphorin3B. Both Sema3B and Sema3F proteins are
           candidate tumor suppressors that are down-regulated in
           highly metastatic tumors. Two receptor families, the
           neuropilins and plexins, have been implicated in
           mediating the actions of semaphorins 3B and 3F. Sema3F
           is a member of the class 3 semaphorin family of
           proteins. Semaphorins are regulatory molecules in the
           development of the nervous system and in axonal
           guidance. They also play important roles in other
           biological processes, such as angiogenesis, immune
           regulation, respiration systems and cancer. The Sema
           domain is located at the N-terminus and contains four
           disulfide bonds formed by eight conserved cysteine
           residues. It serves as a receptor-recognition and
           -binding module.
          Length = 470

 Score = 32.1 bits (73), Expect = 0.38
 Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 1/34 (2%)

Query: 132 GAYPPDLSYITMARHGAEDYVFHLLTGYMDPPAG 165
           GAY P  +YI   R  AEDY+F L    ++   G
Sbjct: 89  GAYNPVCAYINRGRR-AEDYMFRLEPDKLESGKG 121


>gnl|CDD|239510 cd03418, GRX_GRXb_1_3_like, Glutaredoxin (GRX) family, GRX
           bacterial class 1 and 3 (b_1_3)-like subfamily; composed
           of bacterial GRXs, approximately 10 kDa in size, and
           proteins containing a GRX or GRX-like domain. GRX is a
           glutathione (GSH) dependent reductase, catalyzing the
           disulfide reduction of target proteins such as
           ribonucleotide reductase. It contains a redox active
           CXXC motif in a TRX fold and uses a similar dithiol
           mechanism employed by TRXs for intramolecular disulfide
           bond reduction of protein substrates. Unlike TRX, GRX
           has preference for mixed GSH disulfide substrates, in
           which it uses a monothiol mechanism where only the
           N-terminal cysteine is required. The flow of reducing
           equivalents in the GRX system goes from NADPH -> GSH
           reductase -> GSH -> GRX -> protein substrates. By
           altering the redox state of target proteins, GRX is
           involved in many cellular functions including DNA
           synthesis, signal transduction and the defense against
           oxidative stress. Different classes are known including 
           E. coli GRX1 and GRX3, which are members of this
           subfamily.
          Length = 75

 Score = 27.9 bits (63), Expect = 1.4
 Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 13/63 (20%)

Query: 56  EVY-KNVCAACHSARFICYRNLVGVSHTEAEAKREAEEIMVEDGPNEKGEMFKRPGKLSD 114
           E+Y K  C  C  A+ +  +   GV +         EEI V+  P  + EM  R G    
Sbjct: 3   EIYTKPNCPYCVRAKALLDKK--GVDY---------EEIDVDGDPALREEMINRSGGRR- 50

Query: 115 TFP 117
           T P
Sbjct: 51  TVP 53


>gnl|CDD|198412 cd10430, BI-1, BAX inhibitor (BI)-1.  Mammalian members of the BAX
           inhibitor (BI)-1 like family of small transmembrane
           proteins have been shown to have an antiapoptotic effect
           either by stimulating the antiapoptotic function of
           Bcl-2, a well-characterized oncogene, or by inhibiting
           the proapoptotic effect of Bax, another member of the
           Bcl-2 family. Their broad tissue distribution and high
           degree of conservation suggests an important regulatory
           role. In plants, BI-1 like proteins play a role in
           pathogen resistance.
          Length = 213

 Score = 29.9 bits (68), Expect = 1.4
 Identities = 8/21 (38%), Positives = 13/21 (61%)

Query: 141 ITMARHGAEDYVFHLLTGYMD 161
           I  A +G  DY++H L  ++D
Sbjct: 176 IEKAENGDRDYIWHALDLFVD 196


>gnl|CDD|151413 pfam10966, DUF2768, Protein of unknown function (DUF2768).  This
           family of proteins with unknown function appear to be
           restricted to Bacillus spp.
          Length = 58

 Score = 27.7 bits (62), Expect = 1.5
 Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 1/32 (3%)

Query: 266 ALQAVGLMTILTAALFYLKRYKFSSLKTRKIS 297
           +  ++GLM  ++    YL RYK  +   + I 
Sbjct: 5   SFGSMGLM-FISVGTIYLSRYKLKNKFLKFIV 35


>gnl|CDD|165425 PHA03154, PHA03154, hypothetical protein; Provisional.
          Length = 304

 Score = 30.0 bits (67), Expect = 1.5
 Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 2/43 (4%)

Query: 204 ALYNEIIEYEDGTPATQSQLAKDVSTFLKWCGEPEHDTRKRMA 246
           A  N+ I   +    T++ L ++VS F +WC E E     RMA
Sbjct: 225 AHCNDCIN--ESIGFTEALLKQEVSAFYEWCLEQEDYEADRMA 265


>gnl|CDD|213279 cd05911, Firefly_Luc_like, Firefly luciferase of light emitting
           insects and 4-Coumarate-CoA Ligase (4CL).  This family
           contains two functionally unique groups of proteins; one
           group is insect firefly luciferases and the other is
           plant 4-coumarate:coenzyme A ligases. However, they
           share significant sequence similarity in spite of their
           functional diversity. Luciferase catalyzes the
           production of light in the presence of MgATP, molecular
           oxygen, and luciferin. In the first step, luciferin is
           activated by acylation of its carboxylate group with
           ATP, resulting in an enzyme-bound luciferyl adenylate.
           In the second step, luciferyl adenylate reacts with
           molecular oxygen, producing an enzyme-bound excited
           state product (Luc=O*) and releasing AMP. This
           excited-state product then decays to the ground state
           (Luc=O), emitting a quantum of visible light.
           4-coumarate:coenzyme A ligase is a key enzyme in the
           phenylpropanoid metabolic pathway for monolignol and
           flavonoid biosynthesis. It catalyzes the synthesis of
           hydroxycinnamate-CoA thioesters in a two-step reaction,
           involving the formation of hydroxycinnamate-AMP
           anhydride and then the nucleophilic substitution of AMP
           by CoA. The phenylpropanoid pathway is one of the most
           important secondary metabolism pathways in plants and
           hydroxycinnamate-CoA thioesters are the precursors of
           lignin and other important phenylpropanoids.
          Length = 487

 Score = 28.7 bits (65), Expect = 3.9
 Identities = 30/120 (25%), Positives = 42/120 (35%), Gaps = 20/120 (16%)

Query: 18  LESSYVQAGDLELHPPHLKWSHSG-----------LLDSFDHASIRRGYEVYKNVCAACH 66
            +S  V   DL      L+   SG           L   F + +I++GY + +   A   
Sbjct: 252 AKSPLVDKYDL----SSLRVIFSGAAPLSKELQEELRKRFPNTTIKQGYGMTETGPATTL 307

Query: 67  SARFICYRNLVGVSHTEAEAKREAEEIMVEDGPNEKGEM-FKRPGKLSDTFPSPYPNEEA 125
           +         VG      EAK   E+     GPNE+GE+  K P            N EA
Sbjct: 308 TPPGDEKPGSVGRLVPNVEAKIVDEDGGKSLGPNERGELCVKGPQI----MKGYLNNPEA 363


>gnl|CDD|224921 COG2010, CccA, Cytochrome c, mono- and diheme variants [Energy
           production and conversion].
          Length = 150

 Score = 27.7 bits (61), Expect = 5.3
 Identities = 11/57 (19%), Positives = 17/57 (29%)

Query: 49  ASIRRGYEVYKNVCAACHSARFICYRNLVGVSHTEAEAKREAEEIMVEDGPNEKGEM 105
           A+   G  ++   CAACH         L+                ++       GEM
Sbjct: 49  AARGAGLALFLGNCAACHGPNLGGAGPLLDGPALAGGDPPYIVWTILHGTRGGWGEM 105


>gnl|CDD|151610 pfam11168, DUF2955, Protein of unknown function (DUF2955).  Some
           members in this family of proteins with unknown function
           annotate the proteins as membrane protein. However, this
           cannot be confirmed.
          Length = 140

 Score = 27.1 bits (61), Expect = 7.3
 Identities = 16/37 (43%), Positives = 18/37 (48%), Gaps = 2/37 (5%)

Query: 255 VLAGGAGALLYAL--QAVGLMTILTAALFYLKRYKFS 289
           VL  G G LL  L  Q   LMT+L A L + K    S
Sbjct: 54  VLTAGVGLLLSGLLQQYPVLMTLLVALLLFFKFRAMS 90


>gnl|CDD|183683 PRK12686, PRK12686, carbamate kinase; Reviewed.
          Length = 312

 Score = 27.7 bits (62), Expect = 8.0
 Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 13/50 (26%)

Query: 77  VGVSHTEAEAKREAEE---IMVEDGPNEKGEMFKRPGKLSDTFPSPYPNE 123
           +G  +TE EAK++AE+      ED     G  ++R        PSP P E
Sbjct: 130 IGPFYTEEEAKQQAEQPGSTFKEDA----GRGYRR------VVPSPKPQE 169


>gnl|CDD|225797 COG3258, COG3258, Cytochrome c [Energy production and conversion].
          Length = 293

 Score = 27.5 bits (61), Expect = 8.7
 Identities = 10/21 (47%), Positives = 12/21 (57%)

Query: 49  ASIRRGYEVYKNVCAACHSAR 69
           A   RG ++Y   CAACH A 
Sbjct: 160 ADPVRGKKLYAEQCAACHGAD 180


>gnl|CDD|217210 pfam02738, Ald_Xan_dh_C2, Molybdopterin-binding domain of aldehyde
           dehydrogenase. 
          Length = 543

 Score = 27.6 bits (62), Expect = 8.7
 Identities = 26/116 (22%), Positives = 33/116 (28%), Gaps = 34/116 (29%)

Query: 131 NGAYPPDLSYITMARHGAEDYVFHLLTGYMDPPAGDYVF---------HLLTG------- 174
             AY   +S    A +      F   TG    P   + +           LTG       
Sbjct: 424 VAAYGVSVSLSATAAYATPPTGFEPGTGSYGTPFFYFTYGAAAVEVEVDCLTGDVKVLRT 483

Query: 175 --YMDP-----PAGV--QIREGLYFNPYFLGGAIGMAQALYNEIIEYEDGTPATQS 221
              MD      PA    QI  G            G+  AL  EI+    G   T+S
Sbjct: 484 DIVMDCGTSLNPAIDEGQIEGGF---------VQGIGLALMEEIVYDPGGNLLTRS 530


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.319    0.136    0.411 

Gapped
Lambda     K      H
   0.267   0.0698    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,138,305
Number of extensions: 1589927
Number of successful extensions: 1640
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1630
Number of HSP's successfully gapped: 24
Length of query: 305
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 208
Effective length of database: 6,635,264
Effective search space: 1380134912
Effective search space used: 1380134912
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 (21.7 bits)
S2: 59 (26.6 bits)