RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|255764512|ref|YP_003065529.2| preprotein tranlocase protein
[Candidatus Liberibacter asiaticus str. psy62]
         (108 letters)



>gnl|CDD|145709 pfam02699, YajC, Preprotein translocase subunit.  See.
          Length = 83

 Score = 92.5 bits (231), Expect = 2e-20
 Identities = 33/83 (39%), Positives = 56/83 (67%), Gaps = 1/83 (1%)

Query: 19  SPLEMAGLFFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRRGDSIVTAAGIVGKVVRVIDD 78
           S L       ++  ++YFLLIRPQ+++ +   EML +L++GD +VT  GI GK+V+ +DD
Sbjct: 1   SGLSSLLPLVLIFAIFYFLLIRPQQKRQKEHKEMLSSLKKGDEVVTIGGIHGKIVK-VDD 59

Query: 79  LELEVEIAENVRVRVVRSFVSEV 101
             + +EIA+ V+V+V +S ++ V
Sbjct: 60  DTVVLEIADGVKVKVDKSAIARV 82


>gnl|CDD|32047 COG1862, YajC, Preprotein translocase subunit YajC [Intracellular
           trafficking and secretion].
          Length = 97

 Score = 84.5 bits (209), Expect = 5e-18
 Identities = 29/94 (30%), Positives = 56/94 (59%), Gaps = 1/94 (1%)

Query: 15  TSATSPLEMAGLFFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRRGDSIVTAAGIVGKVVR 74
               S L +     ++  ++YFL+IRPQR++++   E+L +L++GD +VT  GIVG V +
Sbjct: 3   MQGGSGLVLLLPLVLIFAIFYFLIIRPQRKRMKEHQELLNSLKKGDEVVTIGGIVGTVTK 62

Query: 75  VIDDLELEVEIAENVRVRVVRSFVSEVQSKSEPV 108
           V DD  +E+E+ +  +++  +  ++ V  K +  
Sbjct: 63  VGDD-TVEIELGDGTKIKFEKEAIATVLEKGDLK 95


>gnl|CDD|32283 COG2100, COG2100, Predicted Fe-S oxidoreductase [General function
           prediction only].
          Length = 414

 Score = 27.2 bits (60), Expect = 0.90
 Identities = 16/72 (22%), Positives = 35/72 (48%), Gaps = 12/72 (16%)

Query: 37  LLIRPQRQQLQRRAEMLRNLRRGDSI---VTAAGIV---------GKVVRVIDDLELEVE 84
           L+++P    +  R  + +  +RG+ +   V   G +          +V+ VI+  E  + 
Sbjct: 333 LILKPGEFGMHPRPRLPKPFKRGEVVKAEVVLPGRLKGEMLAVARDRVIAVINSNEGALL 392

Query: 85  IAENVRVRVVRS 96
           + + V+VR+VR+
Sbjct: 393 VGDRVKVRIVRT 404


>gnl|CDD|30878 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
           [Translation, ribosomal structure and biogenesis].
          Length = 509

 Score = 26.7 bits (59), Expect = 1.5
 Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 2/48 (4%)

Query: 56  LRRGDSIVTAAGIVGKVVRVIDDLELEVEIAENVRVRVVRSFVSEVQS 103
           L++GD IV A G  G+V  ++DDL   ++ A      V    +SEV +
Sbjct: 208 LKKGDIIV-AGGEYGRVRTMVDDLGKPIKEAG-PSKPVEILGLSEVPA 253


>gnl|CDD|28760 cd03118, alpha_CA_V, Carbonic anhydrase alpha, CA isozyme V_like
           subgroup.  Carbonic anhydrases (CAs) are zinc-containing
           enzymes that catalyze the reversible hydration of carbon
           dioxide in a two-step mechanism: a nucleophilic attack
           of a zinc-bound hydroxide ion on carbon dioxide,
           followed by the regeneration of the active site by
           ionization of the zinc-bound water molecule and removal
           of a proton from the active site. They are ubiquitous
           enzymes involved in fundamental processes like
           photosynthesis, respiration, pH homeostasis and ion
           transport. Most alpha CAs are monomeric enzymes. The
           zinc ion is complexed by three histidines. This
           vertebrate subgroup comprises isozyme V. CA V is the
           mitochondrial isozyme, which may play a role in
           gluconeogenesis and ureagenesis and possibly also in
           lipogenesis..
          Length = 236

 Score = 26.1 bits (57), Expect = 2.2
 Identities = 11/34 (32%), Positives = 19/34 (55%)

Query: 30  LAVVWYFLLIRPQRQQLQRRAEMLRNLRRGDSIV 63
           LAV+  FL +    + LQ+  + L  +R  D++V
Sbjct: 117 LAVIGVFLKLGAHHEGLQKLVDALPEVRHKDTVV 150


>gnl|CDD|173935 cd08176, LPO, Lactadehyde:propanediol oxidoreductase (LPO)
          catalyzes the interconversion between L-lactaldehyde
          and L-1,2-propanediol in Escherichia coli and other
          enterobacteria.  Lactadehyde:propanediol oxidoreductase
          (LPO) is a member of the group III iron-activated
          dehydrogenases which catalyze the interconversion
          between L-lactaldehyde and L-1,2-propanediol in
          Escherichia coli and other enterobacteria. L-Fucose and
          L-rhamnose is used by Escherichia coli through an
          inducible pathway mediated by the fucose regulon
          comprising four linked oeprons fucO, fucA, fucPIK, and
          fucR. The fucA-encoded aldolase catalyzes the formation
          of dihydroxyacetone phosphate and L-lactaldehyde. Under
          anaerobic conditions, with NADH as a cofactor,
          lactaldehyde is converted by a fucO-encoded
          Lactadehyde:propanediol oxidoreductase (LPO) to
          L-1,2-propanediol, which is excreted as a fermentation
          product. In mutant strains, E. coli adapted to grow on
          L-1,2-propanediol, FucO catalyzes the oxidation of the
          polyol to L-lactaldehyde. FucO is induced regardless of
          the respiratory conditions of the culture, remains
          fully active in the absence of oxygen. In the presence
          of oxygen, this enzyme becomes oxidatively inactivated
          by a metal-catalyzed oxidation mechanism. FucO is an
          iron-dependent metalloenzyme that is inactivated by
          other metals, such as zinc, copper, or cadmium. This
          enzyme can also reduces glycol aldehyde with similar
          efficiency.  Beside L-1,2-propanediol, the enzyme is
          also able to oxidize methanol as alternative
          substrates.
          Length = 377

 Score = 25.6 bits (57), Expect = 3.2
 Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 5/34 (14%)

Query: 62 IVT-----AAGIVGKVVRVIDDLELEVEIAENVR 90
          IVT       G+V KV  V+D+  ++  I + V+
Sbjct: 33 IVTDKGLVKIGVVEKVTDVLDEAGIDYVIYDGVK 66


>gnl|CDD|176214 cd08252, AL_MDR, Arginate lyase and other MDR family members.  This
           group contains a structure identified as an arginate
           lyase. Other members are identified quinone reductases,
           alginate lyases, and other proteins related to the
           zinc-dependent dehydrogenases/reductases. QOR catalyzes
           the conversion of a quinone and NAD(P)H to a
           hydroquinone and NAD(P+. Quinones are cyclic diones
           derived from aromatic compounds. Membrane bound QOR acts
           in the respiratory chains of bacteria and mitochondria,
           while soluble QOR acts to protect from toxic quinones
           (e.g. DT-diaphorase) or as a soluble eye-lens protein in
           some vertebrates (e.g. zeta-crystalin). QOR reduces
           quinones through a semi-quinone intermediate via a
           NAD(P)H-dependent single electron transfer. QOR is a
           member of the medium chain dehydrogenase/reductase
           family, but lacks the zinc-binding sites of the
           prototypical alcohol dehydrogenases of this group.
           Alcohol dehydrogenase in the liver converts ethanol and
           NAD+ to acetaldehyde and NADH, while in yeast and some
           other microorganisms ADH catalyzes the conversion
           acetaldehyde to ethanol in alcoholic fermentation. ADH
           is a member of the medium chain alcohol dehydrogenase
           family (MDR), which has a NAD(P)(H)-binding domain in a
           Rossmann fold of a beta-alpha form.  The NAD(H)-binding
           region is comprised of 2 structurally similar halves,
           each of which contacts a mononucleotide.  The N-terminal
           catalytic domain has a distant homology to GroES. These
           proteins typically form dimers (typically higher plants,
           mammals) or tetramers (yeast, bacteria), and have 2
           tightly bound zinc atoms per subunit, a catalytic zinc
           at the active site and a structural zinc in a lobe of
           the catalytic domain. NAD(H) binding occurs in the cleft
           between the catalytic and coenzyme-binding domains at
           the active site, and coenzyme binding induces a
           conformational closing of this cleft. Coenzyme binding
           typically precedes and contributes to substrate binding.
            In human ADH catalysis, the zinc ion helps coordinate
           the alcohol, followed by deprotonation of  a histidine,
           the ribose of NAD, a serine, then the alcohol, which
           allows the transfer of a hydride to NAD+, creating NADH
           and a zinc-bound aldehyde or ketone. In yeast and some
           bacteria, the active site zinc binds an aldehyde,
           polarizing it, and leading to the reverse reaction.
          Length = 336

 Score = 25.2 bits (56), Expect = 4.0
 Identities = 17/89 (19%), Positives = 30/89 (33%), Gaps = 28/89 (31%)

Query: 13  AITSATSPLEMAGLFF-VLAVVWYFLLIRP---------QRQQLQRRAEML--------- 53
            I     PL++  L     +  W F+  R          Q + L   A++L         
Sbjct: 246 LIVDPQEPLDLGPLKSKSASFHWEFMFTRSMFQTPDMIEQHEILNEVADLLDAGKLKTTL 305

Query: 54  ---------RNLRRGDSIVTAAGIVGKVV 73
                     NLR   +++ +   +GK+V
Sbjct: 306 TETLGPINAENLREAHALLESGKTIGKIV 334


>gnl|CDD|146989 pfam04612, GspM, General secretion pathway, M protein.  This is a
          family of membrane proteins involved in the secretion
          of a number of molecules in Gram-negative bacteria. The
          precise function of these proteins is unknown, though
          in Vibrio cholerae, the EpsM protein interacts with the
          EpsL protein, and also forms homodimers.
          Length = 159

 Score = 25.3 bits (56), Expect = 4.1
 Identities = 9/36 (25%), Positives = 15/36 (41%)

Query: 23 MAGLFFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRR 58
                +L V+ Y  L +P  Q+  R    L+  R+
Sbjct: 20 AVLGAVLLLVLLYLGLWQPLSQRRARAQRRLQAARQ 55


>gnl|CDD|110924 pfam01972, SDH_sah, Serine dehydrogenase proteinase.  This family
          of archaebacterial proteins, formerly known as DUF114,
          has been found to be a serine dehydrogenase proteinase
          distantly related to ClpP proteinases that belong to
          the serine proteinase superfamily. The family has a
          catalytic triad of Ser, Asp, His residues, which shows
          an altered residue ordering compared with the ClpP
          proteinases but similar to that of the carboxypeptidase
          clan.
          Length = 286

 Score = 24.8 bits (54), Expect = 4.9
 Identities = 11/36 (30%), Positives = 21/36 (58%), Gaps = 2/36 (5%)

Query: 23 MAGLFFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRR 58
          ++ LF+ L  ++++L+I PQ +  Q     LR +R 
Sbjct: 10 LSSLFWFL--LFFYLIIAPQMKMRQLIMARLRCIRE 43


>gnl|CDD|132877 cd07180, RNaseH_typeII_Archaea_like, Archaeal ribonuclease  HII.
           Ribonuclease (RNase) H is classified into two families,
           type I (prokaryotic RNase HI, eukaryotic RNase H1 and
           viral RNase H) and type II (prokaryotic RNase HII and
           HIII, archaeal RNase HII and eukaryotic RNase H2/HII).
           RNase H endonucleolytically hydrolyzes an RNA strand
           when it is annealed to a complementary DNA strand in the
           presence of divalent cations, in DNA replication or
           repair. Some archaeal RNase HII show broad divalent
           cation specificity. It is proposed that three of the
           four acidic residues at the active site are involved in
           metal binding and the fourth one involved in the
           catalytic process in archaea. Most archaeal genomes
           contain multiple RNase H genes. Despite a lack of
           evidence for homology from sequence comparisons, type I
           and type II RNase H share a common fold and similar
           steric configurations of the four acidic active-site
           residues, suggesting identical or very similar catalytic
           mechanisms. It appears that type I and type II RNases H
           also have overlapping functions in cells, as
           over-expression of Escherichia coli RNase HII can
           complement an RNase HI deletion phenotype in E. coli.
          Length = 204

 Score = 24.5 bits (54), Expect = 5.9
 Identities = 10/23 (43%), Positives = 16/23 (69%), Gaps = 2/23 (8%)

Query: 62  IVTAAGIVGKVVR--VIDDLELE 82
           +V+AA I+ KV R   I++L+ E
Sbjct: 139 VVSAASIIAKVERDREIEELKEE 161


>gnl|CDD|173650 cd05094, PTKc_TrkC, Catalytic domain of the Protein Tyrosine
          Kinase, Tropomyosin Related Kinase C.  Protein Tyrosine
          Kinase (PTK) family; Tropomyosin Related Kinase C
          (TrkC); 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. TrkC is
          a member of the Trk subfamily of proteins, which are
          receptor tyr kinases (RTKs) containing an extracellular
          region with arrays of leucine-rich motifs flanked by
          two cysteine-rich clusters followed by two
          immunoglobulin-like domains, a transmembrane segment,
          and an intracellular catalytic domain. Binding of TrkC
          to its ligand, neurotrophin 3 (NT3), results in
          receptor oligomerization and activation of the
          catalytic domain. TrkC is broadly expressed in the
          nervous system and in some non-neural tissues including
          the developing heart. NT3/TrkC signaling plays an
          important role in the innervation of the cardiac
          conducting system and the development of smooth muscle
          cells. Mice deficient with NT3 and TrkC have multiple
          heart defects. NT3/TrkC signaling is also critical for
          the development and maintenance of enteric neurons that
          are important for the control of gut peristalsis.
          Length = 291

 Score = 24.6 bits (53), Expect = 6.4
 Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%)

Query: 43 RQQLQRRAEMLRNLRRGDSIVTAAGIVG 70
          R+  QR AE+L NL+  + IV   G+ G
Sbjct: 51 RKDFQREAELLTNLQH-EHIVKFYGVCG 77


>gnl|CDD|173769 cd08229, STKc_Nek7, Catalytic domain of the Protein
           Serine/Threonine Kinase, Never In Mitosis gene A-related
           kinase 7.  Serine/Threonine Kinases (STKs), Never In
           Mitosis gene A (NIMA)-related kinase 7 (Nek7) subfamily,
           catalytic (c) domain. STKs catalyze the transfer of the
           gamma-phosphoryl group from ATP to serine/threonine
           residues on protein substrates. The Nek7 subfamily is
           one of a family of 11 different Neks (Nek1-11) that are
           involved in cell cycle control. The Nek family is part
           of a larger superfamily that includes the catalytic
           domains of other protein STKs, protein tyrosine kinases,
           RIO kinases, aminoglycoside phosphotransferase, choline
           kinase, and phosphoinositide 3-kinase. Nek7 is required
           for mitotic spindle formation and cytokinesis. It is
           enriched in the centrosome and is critical for
           microtubule nucleation. Nek7 is activated by Nek9 during
           mitosis, and may regulate the p70 ribosomal S6 kinase.
          Length = 267

 Score = 24.6 bits (53), Expect = 6.5
 Identities = 11/38 (28%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 33  VW-YFLLIRPQRQQLQRRAEMLRNLRRGDSIVTAAGIV 69
           VW YF+ +    + +  R  M R+++  +  +TA G+V
Sbjct: 108 VWKYFVQLCSALEHMHSRRVMHRDIKPANVFITATGVV 145


>gnl|CDD|132878 cd07181, RNaseH_typeII_eukaryota_like, Eukaryotic Ribonuclease HII;
           putative role in Okazaki fragment removal during
           replication.  Ribonuclease (RNase) HII
           endonucleolytically hydrolyzes an RNA strand when it is
           annealed to a complementary DNA strand in the presence
           of divalent cations, in DNA replication and repair.
           RNase H is classified into two families, type I
           (prokaryotic RNase HI, eukaryotic RNase H1 and viral
           RNase H) and type II (prokaryotic RNase HII and HIII,
           and eukaryotic RNase H2/HII). The enzyme can be found in
           bacteria, archaea, and eukaryotes. Most prokaryotic and
           eukaryotic genomes contain multiple RNase H genes.
           Despite a lack of evidence for homology from sequence
           comparisons, type I and type II RNase H share a common
           fold and similar steric configurations of the four
           acidic active-site residues, suggesting identical or
           very similar catalytic mechanisms. Eukaryotic RNase HII
           is a type II RNase H that is active during replication
           and is believed to play a role in removal of Okazaki
           fragment primers and single ribonucleotides in DNA-DNA
           duplexes. Eukaryotic RNase HII is functional when it
           forms a complex with two other accessory proteins. It is
           speculated that the two accessory subunits are required
           for correct folding of the catalytic subunit of RNase
           HII.  It appears that type I and type II RNases H also
           have overlapping functions in cells, as over-expression
           of Escherichia coli RNase HII can complement an RNase HI
           deletion phenotype in E. coli.
          Length = 216

 Score = 24.5 bits (54), Expect = 7.3
 Identities = 9/13 (69%), Positives = 10/13 (76%)

Query: 62  IVTAAGIVGKVVR 74
           IV+AA IV KV R
Sbjct: 145 IVSAASIVAKVTR 157


>gnl|CDD|39694 KOG4494, KOG4494, KOG4494, Cell surface ATP diphosphohydrolase
           Apyrase [Nucleotide transport and metabolism].
          Length = 352

 Score = 24.2 bits (52), Expect = 7.3
 Identities = 11/80 (13%), Positives = 31/80 (38%), Gaps = 4/80 (5%)

Query: 27  FFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRRGDSIVTAAGIVGKVVRVIDDLELEVEIA 86
            FV A+++Y         +  R+ E + +           GI  ++  +I DL+ + +  
Sbjct: 16  GFVTAILFYSG---SHFNKSGRQEEHIAHANLYSPKKFDDGIEYRIA-LIADLDTDSKDG 71

Query: 87  ENVRVRVVRSFVSEVQSKSE 106
           +  +  + + +++       
Sbjct: 72  KTWKSYLKKGYLTVSADHKH 91


>gnl|CDD|143978 pfam00223, PsaA_PsaB, Photosystem I psaA/psaB protein. 
          Length = 682

 Score = 24.3 bits (53), Expect = 7.6
 Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 2/32 (6%)

Query: 6   YAQSDAPAITSATSPLEMAGLFFVLA-VVWYF 36
           +A S +  I S  S L + GL F+ A  VW F
Sbjct: 588 WANS-SQVINSYGSLLSVYGLMFLGAHFVWAF 618


>gnl|CDD|145017 pfam01654, Bac_Ubq_Cox, Bacterial Cytochrome Ubiquinol Oxidase.
           This family are the alternative oxidases found in many
           bacteria which oxidize ubiquinol and reduce oxygen as
           part of the electron transport chain. This family is the
           subunit I of the oxidase E. coli has two copies of the
           oxidase, bo and bd', both of which are represented here
           In some nitrogen fixing bacteria, e.g. Klebsiella
           pneumoniae this oxidase is responsible for removing
           oxygen in microaerobic conditions, making the oxidase
           required for nitrogen fixation. This subunit binds a
           single b-haem, through ligands at His186 and Met393
           (using SW:P11026 numbering). In addition His19 is a
           ligand for the haem b found in subunit II.
          Length = 430

 Score = 24.0 bits (53), Expect = 9.2
 Identities = 13/44 (29%), Positives = 19/44 (43%)

Query: 1   MFTTVYAQSDAPAITSATSPLEMAGLFFVLAVVWYFLLIRPQRQ 44
           +  T  A S   A     S +    L+ VL V   +LL+R  R+
Sbjct: 383 LLRTADAVSPVSAGQVLFSLIGFTLLYAVLFVAEVYLLLRYARK 426


  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    0.135    0.368 

Gapped
Lambda     K      H
   0.267   0.0748    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,199,201
Number of extensions: 58268
Number of successful extensions: 340
Number of sequences better than 10.0: 1
Number of HSP's gapped: 337
Number of HSP's successfully gapped: 39
Length of query: 108
Length of database: 6,263,737
Length adjustment: 75
Effective length of query: 33
Effective length of database: 4,643,062
Effective search space: 153221046
Effective search space used: 153221046
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: 40 (21.6 bits)
S2: 51 (23.4 bits)