RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780853|ref|YP_003065266.1| NADH dehydrogenase subunit B
[Candidatus Liberibacter asiaticus str. psy62]
         (185 letters)



>gnl|CDD|30726 COG0377, NuoB, NADH:ubiquinone oxidoreductase 20 kD subunit and
           related Fe-S oxidoreductases [Energy production and
           conversion].
          Length = 194

 Score =  274 bits (703), Expect = 7e-75
 Identities = 108/161 (67%), Positives = 124/161 (77%)

Query: 21  KVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLE 80
           +           +  KG L+T VD+L+ W R  SL  +TFGLACCAVEMM     RYDLE
Sbjct: 4   EEQDPMGDPVEALLSKGVLLTKVDKLINWGRKNSLWPVTFGLACCAVEMMATFASRYDLE 63

Query: 81  RFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSY 140
           RFG  PRASPRQ+D+MIVAGTLTNKMA ALRRVYDQMPEP++VISMGSCAN GG Y  SY
Sbjct: 64  RFGEVPRASPRQADLMIVAGTLTNKMAPALRRVYDQMPEPKWVISMGSCANSGGMYWNSY 123

Query: 141 SVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRVG 181
           SVV+G DR+VPVD+Y+PGCPP  EAL+YGILLLQ+KIRR G
Sbjct: 124 SVVQGVDRVVPVDVYIPGCPPRPEALLYGILLLQEKIRREG 164


>gnl|CDD|36900 KOG1687, KOG1687, KOG1687, NADH-ubiquinone oxidoreductase,
           NUFS7/PSST/20 kDa subunit [Energy production and
           conversion].
          Length = 168

 Score =  254 bits (649), Expect = 1e-68
 Identities = 109/143 (76%), Positives = 128/143 (89%)

Query: 38  FLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMI 97
           +++  +D L+ WAR GSL  +TFGLACCAVEMM  + PRYD++R+G   RASPRQ+D++I
Sbjct: 17  YVLARLDDLLNWARRGSLWPLTFGLACCAVEMMHLAAPRYDMDRYGVVFRASPRQADLII 76

Query: 98  VAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVP 157
           VAGTLTNKMA ALR+VYDQMPEPR+VISMGSCANGGGYYHYSYSVVRGCDRI+PVDIYVP
Sbjct: 77  VAGTLTNKMAPALRKVYDQMPEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIPVDIYVP 136

Query: 158 GCPPTAEALIYGILLLQKKIRRV 180
           GCPPTAEAL+YGIL LQKKI+R+
Sbjct: 137 GCPPTAEALLYGILQLQKKIKRI 159


>gnl|CDD|176965 CHL00023, ndhK, NADH dehydrogenase subunit K.
          Length = 225

 Score =  166 bits (421), Expect = 4e-42
 Identities = 71/142 (50%), Positives = 103/142 (72%), Gaps = 5/142 (3%)

Query: 41  TSVDQLVTWARTGSLMWMTFGLACCAVEMMQASM--PRYDLERFGFAPRASPRQSDVMIV 98
           T+++ L  W+R  SL  + +G +CC +E   AS+   R+D +R+G  PR+SPRQ+D+++ 
Sbjct: 20  TTLNDLSNWSRLSSLWPLLYGTSCCFIEF--ASLIGSRFDFDRYGLVPRSSPRQADLILT 77

Query: 99  AGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHY-SYSVVRGCDRIVPVDIYVP 157
           AGT+T KMA +L R+Y+QMPEP+YVI+MG+C   GG +   SYS VRG D+++PVD+Y+P
Sbjct: 78  AGTVTMKMAPSLVRLYEQMPEPKYVIAMGACTITGGMFSTDSYSTVRGVDKLIPVDVYLP 137

Query: 158 GCPPTAEALIYGILLLQKKIRR 179
           GCPP  EA+I  I  L+KKI R
Sbjct: 138 GCPPKPEAVIDAITKLRKKISR 159


>gnl|CDD|33071 COG3260, COG3260, Ni,Fe-hydrogenase III small subunit [Energy
           production and conversion].
          Length = 148

 Score =  139 bits (351), Expect = 5e-34
 Identities = 49/115 (42%), Positives = 77/115 (66%)

Query: 65  CAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVI 124
           C +E++ A  PRYD ERFG     SPR +D+++V G +T +M   L++ Y+ MPEP+ VI
Sbjct: 22  CDIEILAALSPRYDAERFGIKVVNSPRHADILLVTGAVTRQMREPLKKAYEAMPEPKIVI 81

Query: 125 SMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRR 179
           ++G+CA  GG +  SYSV    D+++PVD+ +PGCPP  EA++ G++    K+ +
Sbjct: 82  AVGACALSGGIFKDSYSVWGPVDKVIPVDVEIPGCPPRPEAILAGLVAALGKLEK 136


>gnl|CDD|144593 pfam01058, Oxidored_q6, NADH ubiquinone oxidoreductase, 20 Kd
           subunit. 
          Length = 124

 Score =  121 bits (306), Expect = 1e-28
 Identities = 44/122 (36%), Positives = 65/122 (53%), Gaps = 14/122 (11%)

Query: 65  CAVEMMQASMPRYDL-----ERFGFAPRASPR----QSDVMIVAGTLTNKMASALRRVYD 115
           C++ ++    P  DL      R+     A PR     +DV++V G +T K   AL R+Y+
Sbjct: 4   CSISLLALHPPLLDLLDLISLRYHIPLMADPREIPEGADVLLVEGAVTRKPKEALERLYE 63

Query: 116 QMPEPRYVISMGSCANGGGYYH----YSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGIL 171
             P+ +YVI++G+CA  GG        SY  VR    +VPVDI +PGCPP  E ++  +L
Sbjct: 64  LAPKAKYVIAVGTCAAFGGIPAAGNNPSYG-VRPVLGVVPVDINIPGCPPHPEWILGTLL 122

Query: 172 LL 173
            L
Sbjct: 123 AL 124


>gnl|CDD|32124 COG1941, FrhG, Coenzyme F420-reducing hydrogenase, gamma subunit
           [Energy production and conversion].
          Length = 247

 Score = 41.1 bits (96), Expect = 2e-04
 Identities = 24/100 (24%), Positives = 41/100 (41%), Gaps = 22/100 (22%)

Query: 94  DVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGG--------------YYHYS 139
           DV +V G++ +     L  V +   + + V+++GSCA  GG                +  
Sbjct: 53  DVALVEGSVCD--EEELELVKELREKAKIVVALGSCAVTGGVQGLRNKSGEELLRPVYGD 110

Query: 140 YSVVRGCDRIVP------VDIYVPGCPPTAEALIYGILLL 173
                  + +VP      VD  +PGCPP+ E +   +  L
Sbjct: 111 AKSTFNEESVVPLGEVIDVDYAIPGCPPSPEEIARALTAL 150


>gnl|CDD|40042 KOG4845, KOG4845, KOG4845, NADH dehydrogenase, subunit 4 [Energy
           production and conversion].
          Length = 452

 Score = 29.5 bits (66), Expect = 0.50
 Identities = 18/77 (23%), Positives = 28/77 (36%), Gaps = 6/77 (7%)

Query: 15  SSCSLEKVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWM------TFGLACCAVE 68
           SS  L + D       S ++H GF++  +  +  W   GS++ M      +  L C A  
Sbjct: 266 SSTCLRQTDLKKLIAYSSVSHMGFVLIGILSITMWGLIGSILLMIAHGLTSSALFCLAGV 325

Query: 69  MMQASMPRYDLERFGFA 85
               S  R      G  
Sbjct: 326 SYDRSGSRMMYFMGGLF 342


>gnl|CDD|30961 COG0616, SppA, Periplasmic serine proteases (ClpP class)
           [Posttranslational modification, protein turnover,
           chaperones / Intracellular trafficking and secretion].
          Length = 317

 Score = 29.7 bits (66), Expect = 0.55
 Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 8/46 (17%)

Query: 105 KMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIV 150
            +A AL+R+  + P    V+S+G  A  GGYY     +    D+IV
Sbjct: 117 LIARALKRLRAKKP---VVVSVGGYAASGGYY-----IALAADKIV 154


>gnl|CDD|144579 pfam01039, Carboxyl_trans, Carboxyl transferase domain.  All of the
           members in this family are biotin dependent
           carboxylases. The carboxyl transferase domain carries
           out the following reaction; transcarboxylation from
           biotin to an acceptor molecule. There are two recognized
           types of carboxyl transferase. One of them uses acyl-CoA
           and the other uses 2-oxoacid as the acceptor molecule of
           carbon dioxide. All of the members in this family
           utilize acyl-CoA as the acceptor molecule.
          Length = 487

 Score = 28.4 bits (64), Expect = 1.1
 Identities = 15/66 (22%), Positives = 24/66 (36%), Gaps = 13/66 (19%)

Query: 105 KMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVD----IYVPGCP 160
            +  A  R    +P+   V   G CA GG Y           D I+ V     +++ G P
Sbjct: 118 LIFGANSRASGVIPQISLV--TGPCAGGGAY------SPALGDFIIMVKGTSPMFLTG-P 168

Query: 161 PTAEAL 166
              + +
Sbjct: 169 DVVKKV 174


>gnl|CDD|34025 COG4303, EutB, Ethanolamine ammonia-lyase, large subunit [Amino
           acid transport and metabolism].
          Length = 453

 Score = 28.0 bits (62), Expect = 1.6
 Identities = 23/91 (25%), Positives = 36/91 (39%), Gaps = 13/91 (14%)

Query: 53  GSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRAS--------PRQSDVMIVAGTLTN 104
           G L  ++ G  CC     +A   + D E       A+        P   DVM+   T + 
Sbjct: 352 GKLSGISMGCDCCYTNHAKAD--QNDNENLMTLLAAAGCNYIMGIPLGDDVMLNYQTTSF 409

Query: 105 KMASALRRVYDQMPEP---RYVISMGSCANG 132
              + +R++    P P   R++  MG  ANG
Sbjct: 410 HDTATVRQLLGLRPIPEFERWLERMGIMANG 440


>gnl|CDD|34408 COG4799, COG4799, Acetyl-CoA carboxylase, carboxyltransferase
           component (subunits alpha and beta) [Lipid metabolism].
          Length = 526

 Score = 27.9 bits (62), Expect = 2.0
 Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 11/50 (22%)

Query: 120 PRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVD----IYVPGCPPTAEA 165
           P+  + MG CA GG Y           D ++ V     +++ G PP  +A
Sbjct: 165 PQISVVMGPCAGGGAY------SPALTDFVIMVRDQSYMFLTG-PPVIKA 207


>gnl|CDD|48203 cd03328, MR_like_3, Mandelate racemase (MR)-like subfamily of the
           enolase superfamily, subgroup 3. Enzymes of this
           subgroup share three conserved carboxylate ligands for
           the essential divalent metal ion (usually Mg2+), two
           aspartates and a glutamate, and conserved catalytic
           residues,  a Lys-X-Lys motif and a conserved
           histidine-aspartate dyad. This subgroup's function is
           unknown..
          Length = 352

 Score = 27.2 bits (60), Expect = 2.6
 Identities = 20/73 (27%), Positives = 29/73 (39%), Gaps = 11/73 (15%)

Query: 44  DQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVA-GTL 102
           +QL  W   G             V+M     PR D +R   A RA    +++ + A G  
Sbjct: 144 EQLSGWVAQG----------IPRVKMKIGRDPRRDPDRVAAARRAIGPDAELFVDANGAY 193

Query: 103 TNKMASALRRVYD 115
           + K A AL R + 
Sbjct: 194 SRKQALALARAFA 206


>gnl|CDD|31926 COG1740, HyaA, Ni,Fe-hydrogenase I small subunit [Energy production
           and conversion].
          Length = 355

 Score = 27.2 bits (60), Expect = 2.9
 Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 7/56 (12%)

Query: 122 YVISMGSCANGGGYYHYSY--SVVRGCDRIV---PVDIYVPGCPPTAEALIYGILL 172
            +I++G+CA+ GG        +       ++   PV I +PGCPP  +  I   LL
Sbjct: 150 AIIAVGTCASWGGIQAAKPNPTGAGPLSEVIKDKPV-INIPGCPPNPD-WIVATLL 203


>gnl|CDD|143861 pfam00079, Serpin, Serpin (serine protease inhibitor).  Structure
           is a multi-domain fold containing a bundle of helices
           and a beta sandwich.
          Length = 368

 Score = 26.0 bits (58), Expect = 6.5
 Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 6/23 (26%)

Query: 23  DADFSRIS------SEITHKGFL 39
            ADFS IS      S++ HK F+
Sbjct: 291 KADFSGISDEPLYVSKVVHKAFI 313


>gnl|CDD|30641 COG0293, FtsJ, 23S rRNA methylase [Translation, ribosomal structure
           and biogenesis].
          Length = 205

 Score = 26.0 bits (57), Expect = 7.2
 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 7/51 (13%)

Query: 129 CANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRR 179
            A  GG+   +   +    +IV VDI +P         I G++ LQ  I  
Sbjct: 53  GAAPGGWSQVAAKKLGAGGKIVAVDI-LPM------KPIPGVIFLQGDITD 96


>gnl|CDD|133216 cd05085, PTKc_Fer, Catalytic domain of the Protein Tyrosine Kinase,
           Fer.  Protein Tyrosine Kinase (PTK) family; Fer kinase;
           catalytic (c) domain. The PTKc family is part of a
           larger superfamily that includes the catalytic domains
           of other kinases such as protein serine/threonine
           kinases, RIO kinases, and phosphoinositide 3-kinase
           (PI3K). PTKs catalyze the transfer of the
           gamma-phosphoryl group from ATP to tyrosine (tyr)
           residues in protein substrates. Fer kinase is a member
           of the Fes subfamily of proteins which are cytoplasmic
           (or nonreceptor) tyr kinases containing an N-terminal
           region with FCH (Fes/Fer/CIP4 homology) and coiled-coil
           domains, followed by a SH2 domain, and a C-terminal
           catalytic domain. Fer kinase is expressed in a wide
           variety of tissues, and is found to reside in both the
           cytoplasm and the nucleus. It plays important roles in
           neuronal polarization and neurite development,
           cytoskeletal reorganization, cell migration, growth
           factor signaling, and the regulation of cell-cell
           interactions mediated by adherens junctions and focal
           adhesions. Fer kinase also regulates cell cycle
           progression in malignant cells.
          Length = 250

 Score = 25.7 bits (56), Expect = 8.1
 Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 17/72 (23%)

Query: 53  GSLMWMTFGLACCAVEMMQASMPRYDLERFGF---APRASPRQSDVMIVAGTLTNKMASA 109
           G L+W TF L  C    M     R  +E+ G+    P+  P             + +   
Sbjct: 181 GILLWETFSLGVCPYPGMTNQQAREQVEK-GYRMSCPQKCP-------------DDVYKV 226

Query: 110 LRRVYDQMPEPR 121
           ++R +D  PE R
Sbjct: 227 MQRCWDYKPENR 238


>gnl|CDD|38595 KOG3385, KOG3385, KOG3385, V-SNARE [Intracellular trafficking,
           secretion, and vesicular transport].
          Length = 118

 Score = 25.6 bits (56), Expect = 9.1
 Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 9/47 (19%)

Query: 19  LEKVDADFSRISSEITHKGFLVTSVDQLVTWARTGS---LMWMTFGL 62
           L+ +D DF   S      GFL  ++ +L T AR      L WM    
Sbjct: 66  LDGMDDDFDSTS------GFLSGTMGRLKTMARRSGISLLCWMAVFS 106


  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    0.136    0.417 

Gapped
Lambda     K      H
   0.267   0.0787    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,250,143
Number of extensions: 114223
Number of successful extensions: 357
Number of sequences better than 10.0: 1
Number of HSP's gapped: 351
Number of HSP's successfully gapped: 17
Length of query: 185
Length of database: 6,263,737
Length adjustment: 88
Effective length of query: 97
Effective length of database: 4,362,145
Effective search space: 423128065
Effective search space used: 423128065
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: 40 (21.5 bits)
S2: 54 (24.5 bits)