RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781064|ref|YP_003065477.1| FeS assembly scaffold SufA
[Candidatus Liberibacter asiaticus str. psy62]
         (116 letters)



>gnl|CDD|30664 COG0316, IscA, Uncharacterized conserved protein [Function
           unknown].
          Length = 110

 Score =  130 bits (329), Expect = 7e-32
 Identities = 45/111 (40%), Positives = 71/111 (63%), Gaps = 1/111 (0%)

Query: 1   MSDIVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIE 60
            + ++T+T+AA  R+K ++     +  G+R+ +K GGC+G +Y ++   D   + D + E
Sbjct: 1   AAMMITLTDAAAARVKALLAKEGEENLGLRVGVKGGGCSGFQYGLEFD-DEINEDDTVFE 59

Query: 61  KDGVKVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPNQVSACGCGQSVEI 111
           +DGVKV +D  SL Y+ GTEID+  + L SGF F NPN  S+CGCG+S  +
Sbjct: 60  QDGVKVVVDPKSLPYLEGTEIDYVEDLLGSGFTFKNPNAKSSCGCGESFSV 110


>gnl|CDD|36336 KOG1120, KOG1120, KOG1120, Fe-S cluster biosynthesis protein ISA1
           (contains a HesB-like domain) [Inorganic ion transport
           and metabolism].
          Length = 134

 Score =  102 bits (255), Expect = 3e-23
 Identities = 41/108 (37%), Positives = 71/108 (65%), Gaps = 2/108 (1%)

Query: 4   IVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDG 63
            +T+T +AV  IK+++ + + +   +RI +K+ GC GL Y ++  T      D+++E+DG
Sbjct: 29  ALTLTPSAVNHIKQLL-SDKPEDVCLRIGVKQRGCNGLSYTLEY-TKTKGKFDEVVEQDG 86

Query: 64  VKVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPNQVSACGCGQSVEI 111
           V+++I+  +LL ++GTE+D+  +KL S FVF NPN    CGCG+S  +
Sbjct: 87  VRIFIEPKALLTLIGTEMDYVDDKLSSEFVFSNPNAKGTCGCGESFSV 134


>gnl|CDD|110518 pfam01521, Fe-S_biosyn, Iron-sulphur cluster biosynthesis.  This
          family is involved in iron-sulphur cluster
          biosynthesis. Its members include proteins that are
          involved in nitrogen fixation such as the HesB and
          HesB-like proteins.
          Length = 91

 Score = 93.8 bits (234), Expect = 9e-21
 Identities = 41/93 (44%), Positives = 59/93 (63%), Gaps = 2/93 (2%)

Query: 5  VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGV 64
          +T+T+AA   IK++  + +G   G+RI ++ GGC+G  Y +    D   +GD++ E+DGV
Sbjct: 1  ITLTDAAAKWIKKL-LDLEGGENGLRIGVRYGGCSGFSYGLTFE-DEAGEGDEVFEQDGV 58

Query: 65 KVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNP 97
           V +D  SL Y+ GTEIDF  E L SGF F NP
Sbjct: 59 TVVVDEKSLPYLEGTEIDFVEELLGSGFTFSNP 91


>gnl|CDD|36335 KOG1119, KOG1119, KOG1119, Mitochondrial Fe-S cluster biosynthesis
           protein ISA2 (contains a HesB-like domain) [Energy
           production and conversion, Intracellular trafficking,
           secretion, and vesicular transport].
          Length = 199

 Score = 81.2 bits (200), Expect = 6e-17
 Identities = 35/113 (30%), Positives = 65/113 (57%), Gaps = 7/113 (6%)

Query: 2   SDIVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLI-E 60
              + ++++   R+KEI  NS    + +R++++ GGC+G +Y   L  DN ++ DD +  
Sbjct: 91  GFNLHLSDSCSKRLKEIYENSP---EFLRLTVEGGGCSGFQYKFRL--DNKINNDDRVFV 145

Query: 61  KDGVKVWIDSASLLYMLGTEIDFKTEKLYSGF-VFHNPNQVSACGCGQSVEIK 112
           ++G +V +D+ SL  + G  +D+  E + S F + +NP+    C CG S +IK
Sbjct: 146 ENGARVVVDNVSLNLLKGATVDYTNELIRSSFRIVNNPSAKQGCSCGSSFDIK 198


>gnl|CDD|32805 COG2986, HutH, Histidine ammonia-lyase [Amino acid transport and
           metabolism].
          Length = 498

 Score = 27.5 bits (61), Expect = 0.83
 Identities = 16/84 (19%), Positives = 29/84 (34%), Gaps = 12/84 (14%)

Query: 3   DIVTMTEAAVYRIKEIVFNSQG--------KAQGIRISLKKGGCAGLEYMVDLVTDN--P 52
           D V+M   A  ++ EI+ N +          AQ + +        G +     V +    
Sbjct: 414 DHVSMATHAARKLLEIIENLRTILAIELLAAAQAVDLRAPLDLSPGTKAAYAAVREKVPF 473

Query: 53  VDGDDLIEKDGVKV--WIDSASLL 74
           +D D     D       + S +L+
Sbjct: 474 LDDDRPFAPDIEAAAALLASGALI 497


>gnl|CDD|36690 KOG1477, KOG1477, KOG1477, SPRY domain-containing proteins [General
           function prediction only].
          Length = 469

 Score = 26.5 bits (58), Expect = 1.7
 Identities = 8/38 (21%), Positives = 12/38 (31%)

Query: 73  LLYMLGTEIDFKTEKLYSGFVFHNPNQVSACGCGQSVE 110
                GTE+    + L    +  N N        + VE
Sbjct: 160 FFTKNGTEVGEIIKPLSPDLLEENGNLAWLFSPNEEVE 197


>gnl|CDD|143256 cd05848, Ig1_Contactin-5, First Ig domain of contactin-5.
           Ig1_Contactin-5: First Ig domain of the neural cell
           adhesion molecule contactin-5. Contactins are comprised
           of six Ig domains followed by four fibronectin type III
           (FnIII) domains, anchored to the membrane by
           glycosylphosphatidylinositol. The different contactins
           show different expression patterns in the central
           nervous system. In rats, a lack of contactin-5 (NB-2)
           results in an impairment of the neuronal activity in the
           auditory system. Contactin-5 is expressed specifically
           in the postnatal nervous system, peaking at about 3
           weeks postnatal. Contactin-5 is highly expressed in the
           adult human brain in the occipital lobe and in the
           amygdala; lower levels of expression have been detected
           in the corpus callosum, caudate nucleus, and spinal
           cord.
          Length = 94

 Score = 25.3 bits (55), Expect = 4.0
 Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 4/31 (12%)

Query: 78  GTEIDFKTEKLYS----GFVFHNPNQVSACG 104
           GTEID +++  YS      +  NP++V   G
Sbjct: 42  GTEIDTESDYRYSLIDGNLIISNPSEVKDSG 72


>gnl|CDD|144450 pfam00858, ASC, Amiloride-sensitive sodium channel. 
          Length = 441

 Score = 24.7 bits (54), Expect = 5.4
 Identities = 17/74 (22%), Positives = 25/74 (33%), Gaps = 10/74 (13%)

Query: 19  VFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGVKV---------WID 69
            FNS    +    S + G   GL  ++D+  D          + G KV         ++D
Sbjct: 178 TFNSGQTGKPPLRSSRPGPGYGLSLVLDVQQDE-YLYSPSTSEAGFKVLIHSPDEYPFVD 236

Query: 70  SASLLYMLGTEIDF 83
           S       GTE   
Sbjct: 237 SLGFSVPPGTETSI 250


>gnl|CDD|176209 cd08247, AST1_like, AST1 is a cytoplasmic protein associated with
           the periplasmic membrane in yeast.  This group contains
           members identified in targeting of yeast membrane
           proteins ATPase. AST1 is a cytoplasmic protein
           associated with the periplasmic membrane in yeast,
           identified as a multicopy suppressor of pma1 mutants
           which cause temperature sensitive growth arrest due to
           the inability of ATPase to target to the cell surface.
           This family is homologous to the medium chain family of
           dehydrogenases and reductases. Medium chain
           dehydrogenases/reductase (MDR)/zinc-dependent alcohol
           dehydrogenase-like family, which contains the
           zinc-dependent alcohol dehydrogenase (ADH-Zn) and
           related proteins, is a diverse group of proteins related
           to the first identified member, class I mammalian ADH.
           MDRs display a broad range of activities and are
           distinguished from the smaller short chain
           dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
           acids of the MDR).  The MDR proteins have 2 domains: a
           C-terminal NAD(P) binding-Rossmann fold domain of an
           beta-alpha form and an N-terminal catalytic domain with
           distant homology to GroES.
          Length = 352

 Score = 24.5 bits (54), Expect = 5.8
 Identities = 18/71 (25%), Positives = 23/71 (32%), Gaps = 6/71 (8%)

Query: 5   VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEY-----MVDLVTDNPVDGDDLI 59
           VT+        K+  FNS          L  G      Y     ++D   D      +LI
Sbjct: 256 VTIVGDYKANYKKDTFNSWDNPSANARKLF-GSLGLWSYNYQFFLLDPNADWIEKCAELI 314

Query: 60  EKDGVKVWIDS 70
               VK  IDS
Sbjct: 315 ADGKVKPPIDS 325


>gnl|CDD|35481 KOG0260, KOG0260, KOG0260, RNA polymerase II, large subunit
           [Transcription].
          Length = 1605

 Score = 24.6 bits (53), Expect = 5.8
 Identities = 13/24 (54%), Positives = 15/24 (62%)

Query: 90  SGFVFHNPNQVSACGCGQSVEIKR 113
           S   F N +QVSAC   Q+VE KR
Sbjct: 749 SKGSFINISQVSACVGQQNVEGKR 772


  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
   0.319    0.137    0.398 

Gapped
Lambda     K      H
   0.267   0.0810    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,338,726
Number of extensions: 61872
Number of successful extensions: 128
Number of sequences better than 10.0: 1
Number of HSP's gapped: 122
Number of HSP's successfully gapped: 11
Length of query: 116
Length of database: 6,263,737
Length adjustment: 81
Effective length of query: 35
Effective length of database: 4,513,408
Effective search space: 157969280
Effective search space used: 157969280
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: 51 (23.3 bits)