RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780140|ref|YP_003064553.1| putative ABC transporter,
substrate-binding protein [Candidatus Liberibacter asiaticus str.
psy62]
         (452 letters)



>gnl|CDD|31652 COG1463, Ttg2C, ABC-type transport system involved in resistance to
           organic solvents, periplasmic component [Secondary
           metabolites biosynthesis, transport, and catabolism].
          Length = 359

 Score = 87.5 bits (216), Expect = 8e-18
 Identities = 57/301 (18%), Positives = 101/301 (33%), Gaps = 21/301 (6%)

Query: 1   MESKNYYTSVGLFVVSILFFSFFSIYWLSRSNQYDGPMAEVIIRIPG-SVDGLSTDSSVR 59
           ME++     VGLF++  L      + WL+      G      +        GL   S VR
Sbjct: 1   METRANRVLVGLFLLLGLLAVLLFVLWLATLPGLPGGTGTYTVTAYFDDAGGLYVGSPVR 60

Query: 60  FNGIPVGRIVGLFLDQEYPNHSLAKALIRPDTPLYPSTTATIRTQGLAGITYIELSTLRK 119
           + G+ VG++  + LD + PN +     I  D P+   +TA+IRT GL G  YIEL+    
Sbjct: 61  YRGVKVGKVASISLDPK-PNGARVTLEIDSDYPIPADSTASIRTTGLLGEKYIELTPGDA 119

Query: 120 EKKTI---FQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHIQKIIENIEKPL 176
               +     I  ER Q  +      G    +    +   +++         +      L
Sbjct: 120 GGPKLRLGATIPLERTQVPIDLEDLLGDLLLLLGGLDP-DRLNAILNEAAAALAGTGPQL 178

Query: 177 TTTIANIETISTVLANNISHIDKMMH-----TTQVTPHSSDSKNTFNTITDLITSLDKMI 231
              + N+   +  L      I  ++         +   S       + +  L  +L    
Sbjct: 179 NALLDNLAQFTDALNARDGDIGALIANLNQLLDSLAAASDQLDRLLDNLATLTAALAARR 238

Query: 232 KAID---------LQKVNQILENIQVSSNNFVKSSDQVINTVHDVR-ETTQTFQEVGQKI 281
            A+D            VN +L   + + N  + +   +   + D      Q    +    
Sbjct: 239 DALDDALAALSALAATVNDLLAENRPNLNQALANLRPLATLLVDYLPGLEQLLHGLPTYA 298

Query: 282 D 282
            
Sbjct: 299 A 299


>gnl|CDD|111376 pfam02470, MCE, mce related protein.  This family of proteins
           contains the mce (mammalian cell entry) proteins from
           Mycobacterium tuberculosis. The archetype (Rv0169), was
           isolated as being necessary for colonisation of, and
           survival within, the macrophage. This family contains
           proteins of unknown function from other bacteria.
          Length = 80

 Score = 57.2 bits (139), Expect = 8e-09
 Identities = 23/69 (33%), Positives = 32/69 (46%), Gaps = 2/69 (2%)

Query: 48  SVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPD-TPLYPSTTATIRTQGL 106
              GL   + VR+ G+PVGR+  + LD +          I PD   +   + A IR+ GL
Sbjct: 11  DAGGLEVGAPVRYRGVPVGRVTSIDLDPD-GGGVRVTLRIDPDVVVIPKDSRAGIRSLGL 69

Query: 107 AGITYIELS 115
            G  YI L 
Sbjct: 70  LGEKYIALD 78


>gnl|CDD|36151 KOG0933, KOG0933, KOG0933, Structural maintenance of chromosome
            protein 2 (chromosome condensation complex Condensin,
            subunit E) [Chromatin structure and dynamics, Cell cycle
            control, cell division, chromosome partitioning].
          Length = 1174

 Score = 34.5 bits (79), Expect = 0.056
 Identities = 37/252 (14%), Positives = 91/252 (36%), Gaps = 23/252 (9%)

Query: 151  AENTSKKISDSSRHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQVTPHS 210
             EN  +++      ++K I ++++ L      I ++ + L N  + +DK+          
Sbjct: 813  RENEYERLQLEHEELEKEISSLKQQLEQLEKQISSLKSELGNLEAKVDKVEKDV------ 866

Query: 211  SDSKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRET 270
                         +       + ID + ++ +L + +   +       +     H+V + 
Sbjct: 867  -------KKAQAELKDQKAKQRDIDTE-ISGLLTSQEKCLSEKSDGELERKKLEHEVTKL 918

Query: 271  TQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIAD-STSNMRSSISAIREITDQRQKII 329
                    ++++ LL         K          D  + +   +   ++++ ++++K+ 
Sbjct: 919  ESEKANARKEVEKLLKKHEWIGDEKRLFGKKGTDYDFESYDPHEAREELKKLQEKKEKLE 978

Query: 330  STINTIENITSNLNDSSQKFAELMSKINNI----SALKENNSLFKDAQRAMHTFRDTSEK 385
             T+N        L  + +K A L +K   I    S +K+      + +R         EK
Sbjct: 979  KTVNP--KNMDMLERAEEKEAALKTKKEIIEKDKSKIKKTIEKLDEKKR--EELNKAWEK 1034

Query: 386  INRYIPSIGNNL 397
            +N+   SI + L
Sbjct: 1035 VNKDFGSIFSTL 1046


>gnl|CDD|37815 KOG2604, KOG2604, KOG2604, Subunit of cis-Golgi transport vesicle
           tethering complex - Sec34p [Intracellular trafficking,
           secretion, and vesicular transport].
          Length = 733

 Score = 33.8 bits (77), Expect = 0.091
 Identities = 25/118 (21%), Positives = 46/118 (38%), Gaps = 10/118 (8%)

Query: 269 ETTQTFQEVGQKIDHLLSDFSSKMK-SKETSAFLENIADSTSNMRSSISAIREITDQRQK 327
           E      +    +D LLS        S++TSA  E    +   +    S + E+ +  +K
Sbjct: 106 ECDAILDQTNNALDTLLSLQKKFEFVSQKTSALHE----ACEQLLEEQSKLSELAEGIRK 161

Query: 328 IISTINTIENITSNLND-----SSQKFAELMSKINNISALKENNSLFKDAQRAMHTFR 380
            +     +E +   LN          F E+++K++      E N  FKDA   +  ++
Sbjct: 162 KLHYFAELEELNRRLNHPTLSVGKVSFKEMLAKLDECIMFLEENPDFKDAPAYLGKYK 219


>gnl|CDD|177098 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
          Length = 1077

 Score = 33.5 bits (77), Expect = 0.12
 Identities = 52/326 (15%), Positives = 110/326 (33%), Gaps = 57/326 (17%)

Query: 111 YIELSTLRKEKKTIFQIATERNQRAMITATPSGINYFIS---NAENTSKKISDSSRHIQK 167
            +EL    K  K  +          +++A     NY I      +  + K +   + I  
Sbjct: 42  NLELLLFGKNYKLKYPKYN------LLSAKSYDSNYSIQIYLPLKFINLKTNKI-KFINY 94

Query: 168 IIENIEKPLTTTIANI-------ETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNTI 220
           +I N+  P  T              +S ++ +   +  K +            KN+    
Sbjct: 95  LIGNL--PKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIK-----------KNSNKIY 141

Query: 221 TDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQK 280
           +  +          +L K  +I   I++  N            +  ++    T Q++  +
Sbjct: 142 SATLIPNRGSWIKFELDKNKEIW--IRIDKNR-------KKPLIIFLKALGLTDQDIYSR 192

Query: 281 IDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREIT--DQRQKIISTINTIEN- 337
           +    S+F  K+K    ++      +    +  ++S I   T  D  Q + S     +N 
Sbjct: 193 LTK--SEFLKKLKPILLNSNSYTNEEILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNY 250

Query: 338 ---------ITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINR 388
                    I + LN +  +    ++  + +S +        + +     F D     NR
Sbjct: 251 DLGKVGRYKINNKLNLNIPERVRNLTYEDILSII----DKLINLKINKGNFDDIDHLKNR 306

Query: 389 YIPSIGNNLQNFSQSGLNDIQNLVRK 414
            + S+G  LQN  + GL  ++ ++R 
Sbjct: 307 RVRSVGELLQNQFRIGLKRLERILRN 332


>gnl|CDD|112929 pfam04136, Sec34, Sec34-like family.  Sec34 and Sec35 form a
           sub-complex, in a seven protein complex that includes
           Dor1 (pfam04124). This complex is thought to be
           important for tether vesicles to the Golgi.
          Length = 157

 Score = 32.9 bits (75), Expect = 0.19
 Identities = 25/124 (20%), Positives = 44/124 (35%), Gaps = 24/124 (19%)

Query: 266 DVRETTQTFQEVGQKIDHLLSDFSSKMK------------SKETSAFLENIADSTSNMRS 313
                 QTF       D +L   ++               SK+TS   E    +   + +
Sbjct: 4   KKINYLQTFT---NICDQILGQTNNAESTLLSLKEKYEFVSKKTSELSE----ACEQLST 56

Query: 314 SISAIREITDQRQKIISTINTIENITSNLND-----SSQKFAELMSKINNISALKENNSL 368
               + E+ D  QK ++    +E +   L       +S  F E ++K++      E N  
Sbjct: 57  EQMRLSELADGIQKGLTYFAPLEELNRVLRSPTLSVASVSFKEHLTKLDTCIMYIEENPD 116

Query: 369 FKDA 372
           FKD+
Sbjct: 117 FKDS 120


>gnl|CDD|39589 KOG4388, KOG4388, KOG4388, Hormone-sensitive lipase HSL [Lipid
           transport and metabolism].
          Length = 880

 Score = 31.6 bits (71), Expect = 0.50
 Identities = 29/140 (20%), Positives = 53/140 (37%), Gaps = 13/140 (9%)

Query: 90  DTPL--YPSTTATIRTQGLAGITYIELSTLRKE-----KKTIFQIATERNQRA--MITAT 140
           D P+   PS  A  + QG  G   I+  TLR        +T  +   E +  A  +  +T
Sbjct: 635 DIPMRRSPSEAALAQPQGPLGTDSIKNLTLRDLSLTGNSETSSETHPEMSLSAETLSPST 694

Query: 141 PSGINYFISNAENTSKKISDSSRHIQKIIENIEKPLT--TTIANIETISTVLANNISHID 198
           PS +N+ +  A +T  +  D+     +    +  P+     +            +  ++ 
Sbjct: 695 PSDVNFLLPTAPSTPLQQEDAGEE-AEAKNELSPPMDRGLGVRAAFPEGFHARRSSQNLQ 753

Query: 199 KMMHTTQVTPHSSD-SKNTF 217
                T +  +SSD  K+ F
Sbjct: 754 DWFGRTPMELYSSDVPKDPF 773


>gnl|CDD|146867 pfam04437, RINT1_TIP1, RINT-1 / TIP-1 family.  This family includes
           RINT-1, a Rad50 interacting protein which participates
           in radiation induced checkpoint control, as well as the
           TIP-1 protein from yeast that seems to be involved in a
           complex with Sec20p that is required for golgi
           transport.
          Length = 485

 Score = 31.2 bits (71), Expect = 0.65
 Identities = 6/46 (13%), Positives = 20/46 (43%), Gaps = 1/46 (2%)

Query: 203 TTQVTPHSSDSKNTFNTITDLITSLDKMIKAIDLQKV-NQILENIQ 247
             +    SS+       +   I+ L++++     +++  Q+L ++ 
Sbjct: 338 ALESLSPSSELVEALRYLRRRISFLERLLNPAIFRRIWRQLLLSLD 383



 Score = 30.0 bits (68), Expect = 1.5
 Identities = 23/173 (13%), Positives = 53/173 (30%), Gaps = 45/173 (26%)

Query: 284 LLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKIISTINTIENITSNLN 343
            L D +++  S   + F E           +I+++  +    +  I        +     
Sbjct: 275 SLGDIANRTSSNYGALFDE-----------TINSLERLRLDSEGSIVH-----RLVKGFK 318

Query: 344 DSSQKFAELMSKIN-----NISALKENNSLFKDAQRAMHTFRDTSEKINRYIP------- 391
            + + +     KI+     + ++  E+ S   +   A+   R     + R +        
Sbjct: 319 AALRNY----FKISTWSSLSSTSALESLSPSSELVEALRYLRRRISFLERLLNPAIFRRI 374

Query: 392 --SIGNNLQN-----------FSQSGLNDIQNLVRKLQETVNHFDDCLNNFER 431
              +  +L             FS+ G       +R L E  + +     NF +
Sbjct: 375 WRQLLLSLDTYIISSILMLNKFSEGGAAQFHFDMRNLFEVFSLYCMRPENFFK 427


>gnl|CDD|143806 pfam00015, MCPsignal, Methyl-accepting chemotaxis protein (MCP)
           signaling domain.  This domain is thought to transduce
           the signal to CheA since it is highly conserved in very
           diverse MCPs.
          Length = 213

 Score = 30.9 bits (70), Expect = 0.73
 Identities = 22/165 (13%), Positives = 50/165 (30%), Gaps = 48/165 (29%)

Query: 160 DSSRHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNT 219
            +++ I+ +IE I K    + A+I+   T +    + ++              +      
Sbjct: 93  QAAKEIEALIEEIVKQTNDSTASIQQTRTEVEVGSTIVE-------------STGEALKE 139

Query: 220 ITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQ 279
           I D +  +  ++            + I  +S+      DQV   V  + + TQ       
Sbjct: 140 IVDAVAEIADIV------------QEIAAASDEQSAGIDQVNQAVARIDQVTQ------- 180

Query: 280 KIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQ 324
                           + +A +E  A +   +      +     Q
Sbjct: 181 ----------------QNAALVEESAAAAETLEEQAEELTASVAQ 209


>gnl|CDD|34155 COG4477, EzrA, Negative regulator of septation ring formation [Cell
           division and chromosome partitioning].
          Length = 570

 Score = 30.6 bits (69), Expect = 0.88
 Identities = 30/216 (13%), Positives = 80/216 (37%), Gaps = 16/216 (7%)

Query: 214 KNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQT 273
            +    + + +    +++  ++L +  + L  IQ    +     ++ +   + V E    
Sbjct: 254 DSRLERLKEQLVENSELLTQLELDEAEEELGLIQEKIESLYDLLEREVEAKNVVEENLPI 313

Query: 274 FQEVGQKI----DHLLSDFSSKMKS----KETSAFLENIADSTSNMRSSISAIREITDQR 325
             +  +K     +HL  +     +S    +     +         + S +  I E  + +
Sbjct: 314 LPDYLEKAKENNEHLKEEIERVKESYRLAETELGSVRKFEKELKELESVLDEILENIEAQ 373

Query: 326 QKIIS----TINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRD 381
           +   S     +  IE   +++ D  +K  E ++ +         N   +  +  +H  + 
Sbjct: 374 EVAYSELQDNLEEIEKALTDIEDEQEKVQEHLTSLRKDELEAREN--LERLKSKLHEIKR 431

Query: 382 TSEKINRYIPSIGNNLQNFSQSGLNDIQNLVRKLQE 417
             EK N  +P +     +   +  ++IQ+L+++L E
Sbjct: 432 YMEKSN--LPGLPETFLSLFFTAGHEIQDLMKELSE 465


>gnl|CDD|58155 cd03680, MM_CoA_mutase_ICM_like, Coenzyme
           B12-dependent-methylmalonyl coenzyme A (CoA) mutase
           (MCM) family, isobutyryl-CoA mutase (ICM)-like
           subfamily; contains archaeal and bacterial proteins
           similar to the large subunit of Streptomyces
           cinnamonensis coenzyme B12-dependent ICM. ICM from S.
           cinnamonensis is comprised of a large and a small
           subunit. The holoenzyme appears to be an alpha2beta2
           heterotetramer with up to 2 molecules of coenzyme B12
           bound. The small subunit binds coenzyme B12. ICM
           catalyzes the reversible rearrangement of n-butyryl-CoA
           to isobutyryl-CoA, intermediates in fatty acid and
           valine catabolism, which in S. cinnamonensis can be
           converted to methylmalonyl-CoA and used in polyketide
           synthesis..
          Length = 538

 Score = 29.8 bits (67), Expect = 1.4
 Identities = 23/101 (22%), Positives = 39/101 (38%), Gaps = 11/101 (10%)

Query: 106 LAGITYIELSTLRKEKKTIFQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHI 165
           L G  Y+E  T   E++    I        MI A   G  YF        ++I+D++   
Sbjct: 391 LGGSYYVEALTDEIEEEAWKYIDKIDAMGGMIKAIEDG--YF-------QREIADAAYKY 441

Query: 166 QKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQV 206
           QK IE+ E+ +     N   +       +  +D  +   Q+
Sbjct: 442 QKEIESGERIVVG--VNKFVVEEEPPIILLKVDDEVEERQI 480


>gnl|CDD|147584 pfam05478, Prominin, Prominin.  The prominins are an emerging
           family of proteins that among the multispan membrane
           proteins display a novel topology. Mouse prominin and
           human prominin (mouse)-like 1 (PROML1) are predicted to
           contain five membrane spanning domains, with an
           N-terminal domain exposed to the extracellular space
           followed by four, alternating small cytoplasmic and
           large extracellular, loops and a cytoplasmic C-terminal
           domain. The exact function of prominin is unknown
           although in humans defects in PROM1, the gene coding for
           prominin, cause retinal degeneration.
          Length = 809

 Score = 28.8 bits (65), Expect = 2.8
 Identities = 24/95 (25%), Positives = 44/95 (46%), Gaps = 6/95 (6%)

Query: 166 QKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTT-QVTPHSSDSKNTFNTITDLI 224
            +I+EN+E+ +    ++I          I    K+ + T  V P   D K   +++   I
Sbjct: 320 TEILENLEEVVKADFSSIVQEGNSTFEEIP--SKVKNQTSSVVP---DVKAALDSLGTDI 374

Query: 225 TSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQ 259
            S+ + +    L  ++QIL N Q SSN ++   +Q
Sbjct: 375 KSVAEDLPLQVLSVLSQILNNTQSSSNPYLPYVEQ 409



 Score = 28.1 bits (63), Expect = 5.7
 Identities = 21/133 (15%), Positives = 45/133 (33%), Gaps = 39/133 (29%)

Query: 326 QKIISTINTIENITSNLNDSSQ--KFAELMSKINNISALKENNSLFKDAQRAMHTFRDTS 383
            ++   ++T  N+     + S   +    ++        ++N  L+   Q  ++   D +
Sbjct: 502 NELFQVLDTPGNLNPGYLNLSGTLELKINLTISEVYRDCEQNEPLYTVLQ--LNNSYDLN 559

Query: 384 EK--INRYIPSIGN---------------------NLQNFSQSGLNDIQNLVRKLQETVN 420
           E   I +Y P I                       NL++ + SGL+DI            
Sbjct: 560 ELLDIKQYTPEIDQELESLKVNLSTITLLTPEARRNLEDLASSGLDDI------------ 607

Query: 421 HFDDCLNNFERNP 433
           +F + L   ++  
Sbjct: 608 NFSNFLKQIQKPL 620


>gnl|CDD|34381 COG4768, COG4768, Uncharacterized protein containing a divergent
           version of the methyl-accepting chemotaxis-like domain
           [General function prediction only].
          Length = 139

 Score = 28.8 bits (64), Expect = 3.1
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 4/70 (5%)

Query: 236 LQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSK 295
           L K N + E++Q      V + D V + V D+ ++     +  + +    ++   K + K
Sbjct: 58  LHKTNTLAEDVQGK----VATLDPVFDAVKDLGQSVSDLNQSVRHLATRATNAVEKNEKK 113

Query: 296 ETSAFLENIA 305
              A + N+A
Sbjct: 114 IAQAVVSNVA 123


>gnl|CDD|34711 COG5108, RPO41, Mitochondrial DNA-directed RNA polymerase
           [Transcription].
          Length = 1117

 Score = 28.9 bits (64), Expect = 3.4
 Identities = 13/78 (16%), Positives = 35/78 (44%), Gaps = 3/78 (3%)

Query: 343 NDSSQKFAELMSKINNISALKE---NNSLFKDAQRAMHTFRDTSEKINRYIPSIGNNLQN 399
           +   + F   +S  +  ++L E    N  F  +++ + +F D ++     +P I   ++ 
Sbjct: 15  SKIGKDFIIDLSYKSGTASLFEACVYNGDFLRSKQLLKSFIDHNKGDKILLPMINLYIRE 74

Query: 400 FSQSGLNDIQNLVRKLQE 417
             Q G  ++ +++   +E
Sbjct: 75  IIQRGSFELTDVLSNAKE 92


>gnl|CDD|113356 pfam04582, Reo_sigmaC, Reovirus sigma C capsid protein. 
          Length = 326

 Score = 28.7 bits (64), Expect = 3.7
 Identities = 27/124 (21%), Positives = 57/124 (45%), Gaps = 5/124 (4%)

Query: 301 LENIADSTSNMRSSISAI-REITDQRQKIISTINTIENITSNLNDSSQKFAELMSKINNI 359
           L N+  +T+++  S+S I   ++D    +     ++++  + LN        L + ++++
Sbjct: 37  LTNLESATASLSESVSTISSRLSDLSADLQDMTTSLDDAKATLNGLITTVQALQTSVDSL 96

Query: 360 SALKENNSLFKDAQRAMHTFRDTSEKINRYIPSIGNNLQNFSQSGLN--DIQNLVRKLQE 417
           S+   + SL   A  A  +   T+   N     I N   + S +GLN  D++  V+ L+ 
Sbjct: 97  SSELADLSLTVSAHDAAISDLQTTVHANS--TDISNLKSSVSANGLNITDLEQRVKSLES 154

Query: 418 TVNH 421
             +H
Sbjct: 155 GSSH 158


>gnl|CDD|35552 KOG0331, KOG0331, KOG0331, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 519

 Score = 28.4 bits (63), Expect = 3.8
 Identities = 24/122 (19%), Positives = 44/122 (36%), Gaps = 20/122 (16%)

Query: 165 IQKIIENIEKPLTTTIANIETIST---VLANNISHIDKMMHTTQVTPHSSDSKNTFNTIT 221
           I+KI+  I +P   T+    T       LA +  +        Q+   +       + I 
Sbjct: 260 IRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNP-----IQINVGNKKELKANHNIR 314

Query: 222 DLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVI---NTVHDVRETTQTFQEVG 278
            ++   D+  K   L+K+ ++LE+I   S        +VI    T     E  +  +  G
Sbjct: 315 QIVEVCDETAK---LRKLGKLLEDISSDSEG------KVIIFCETKRTCDELARNLRRKG 365

Query: 279 QK 280
             
Sbjct: 366 WP 367


>gnl|CDD|38731 KOG3522, KOG3522, KOG3522, Predicted guanine nucleotide exchange
           factor [Signal transduction mechanisms].
          Length = 925

 Score = 28.4 bits (63), Expect = 3.9
 Identities = 41/227 (18%), Positives = 70/227 (30%), Gaps = 44/227 (19%)

Query: 236 LQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDH-----------L 284
           LQ    +LE +    N   + +D++        E     +E+  + +            L
Sbjct: 150 LQLALTLLETLAEKINEHKRFADEI-------NELQAALREIEVRSELMEDLGAGRRQLL 202

Query: 285 LSDFSSKMK----SKETSAFLENI-ADSTSNMRSSISAIREIT----------------- 322
           L D  S+       K+  AFL      +T   R+S S+ +  T                 
Sbjct: 203 LQDLVSETVYTGRKKDRKAFLFRDLIVNTDLKRASGSSRKPSTAASVVDTAKYKLLWKDP 262

Query: 323 -DQRQKIISTINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMH--TF 379
                 + S    IE I   +    +  A L  K          + L +D QR +H    
Sbjct: 263 LVFADVVKSRAGNIEEIPILIAHLVEDCAHLRQKTKENKVYVGPHQLLQDLQRLLHALDV 322

Query: 380 RDTSEK-INRYIPSIGNNLQNFSQSGLNDIQNLVRKLQETVNHFDDC 425
           R  SE+   R   +  N     +    N +Q L+   +  +      
Sbjct: 323 RRLSERQARRLSLNYQNLNLELAADWPNGLQRLIFVFEAEIGSTPLE 369


>gnl|CDD|36214 KOG0996, KOG0996, KOG0996, Structural maintenance of chromosome
            protein 4 (chromosome condensation complex Condensin,
            subunit C) [Chromatin structure and dynamics, Cell cycle
            control, cell division, chromosome partitioning].
          Length = 1293

 Score = 28.4 bits (63), Expect = 4.5
 Identities = 32/260 (12%), Positives = 88/260 (33%), Gaps = 27/260 (10%)

Query: 113  ELSTLRKEKKTIFQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHIQKIIENI 172
             +  L+ +   I     +  Q+  +      ++   ++    +  I  S R+I K  + +
Sbjct: 886  RIKELQNKIDEIGGEKVQA-QKDKVEKINEQLDKLEADIAKLTVAIKTSDRNIAKAQKKL 944

Query: 173  EKPLTTTIANIETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNTITDLITSLDKMIK 232
             + L   I + E     L   +  +++            + K    ++ ++   L  +  
Sbjct: 945  SE-LEREIEDTEKELDDLTEELKGLEEKA-----AELEKEYKEAEESLKEIKKELRDLKS 998

Query: 233  AI-DLQKVNQILENIQVSSNNFVKSSDQVINTV----------------HDVRETTQTFQ 275
             + +++K    L+  ++   N +++ +  +N +                 ++ ET    +
Sbjct: 999  ELENIKKSENELKAERIDIENKLEAINGELNEIESKIKQPEKELKKLSLCNMTETRPQIE 1058

Query: 276  EVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKIISTINTI 335
                +    L     +    E  A LE   +    +   +  I E   + +  +  +  +
Sbjct: 1059 L-DVESPEELEAEMLEDNINEKIALLEKRVEELREV--DLGVIAEYAKKVELYLKRVAEL 1115

Query: 336  ENITSNLNDSSQKFAELMSK 355
            E  T   ++  +K  EL  +
Sbjct: 1116 EKFTQKRDEHREKLEELRKR 1135


>gnl|CDD|38897 KOG3693, KOG3693, KOG3693, Uncharacterized conserved protein
           [Function unknown].
          Length = 1117

 Score = 28.2 bits (62), Expect = 5.0
 Identities = 18/54 (33%), Positives = 23/54 (42%)

Query: 47  GSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDTPLYPSTTAT 100
           GS+DGLS +S      + VGR + L    + P  SLA   I    P  P     
Sbjct: 114 GSMDGLSMNSFSMPFSVSVGRQMSLTPPLDVPATSLAIHKIPSSAPTLPFKFMK 167


>gnl|CDD|39873 KOG4674, KOG4674, KOG4674, Uncharacterized conserved coiled-coil
           protein [Function unknown].
          Length = 1822

 Score = 28.0 bits (62), Expect = 5.7
 Identities = 41/277 (14%), Positives = 101/277 (36%), Gaps = 19/277 (6%)

Query: 153 NTSKKISD----SSRHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQVTP 208
           +T KK+++        +   +  +++ +      +E  S     N   + ++  +     
Sbjct: 280 STQKKLNELWKSKLEELSHEVAELQRAIEELEKLLEDASERNKENTDQLKELEQS----- 334

Query: 209 HSSDSKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVR 268
            S  ++     ++ L   L+    ++     + ++      +++ ++    +        
Sbjct: 335 LSKLNEKLEKKVSRLEGELEDANDSLSATGESSMVSEKAALASSLIRPGSSLTKLYSKYS 394

Query: 269 ETTQTFQEVGQKIDHLLSDFSSKMK-SKETSAFLENIADSTSNMRSSISAI-REITDQRQ 326
           +  Q  + +  +++ L +  SS  +  K+ +  L+        M+ + + +  E+    Q
Sbjct: 395 KLQQQLESLKLELERLQNILSSFKEEVKQKAPILKEQRSELERMQETKAELSEELDFSNQ 454

Query: 327 KIISTINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKI 386
           KI      +E++   LND  ++   L  +I+++S       L  D  R       +S+  
Sbjct: 455 KIQKLEKELESLKKQLNDLERENKLLEQQISDLSRQVNVLLLELDELRKGSKITVSSDST 514

Query: 387 NRYIPS---IGNNLQNFSQSGLNDIQNLVRKLQETVN 420
                S   I   L  FS     +I  L  K  E +N
Sbjct: 515 ENESDSEEIISERLVEFS-----NINELQEKNVELLN 546


>gnl|CDD|37906 KOG2695, KOG2695, KOG2695, WD40 repeat protein [General function
           prediction only].
          Length = 425

 Score = 27.7 bits (61), Expect = 5.9
 Identities = 15/92 (16%), Positives = 24/92 (26%), Gaps = 7/92 (7%)

Query: 330 STINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRD-------T 382
           S I T E +       +        K  N    +      +   +  ++ RD        
Sbjct: 31  SNIYTKERLKPGKRFENISQKRTKGKGLNPVFNRSTYLFDRQFSQYPYSCRDDRDYCAKN 90

Query: 383 SEKINRYIPSIGNNLQNFSQSGLNDIQNLVRK 414
            + IN     +G  LQ            L  K
Sbjct: 91  LKVINLRQLPVGTELQKIGWLREVTTIILTSK 122


>gnl|CDD|111435 pfam02534, TraG, TraG/TraD family.  These proteins contain a P-loop
           and walker-B site for nucleotide binding. TraG is
           essential for DNA transfer in bacterial conjugation.
           These proteins are thought to mediate interactions
           between the DNA-processing (Dtr) and the mating pair
           formation (Mpf) systems.
          Length = 468

 Score = 27.8 bits (62), Expect = 6.6
 Identities = 30/130 (23%), Positives = 47/130 (36%), Gaps = 24/130 (18%)

Query: 32  NQYDGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDT 91
                P+  V       V  L        +G P    V   LD E+P+  L K       
Sbjct: 272 LTVVSPLLRVFF---QMVVELLYLKLPNGDGRPKE--VLFLLD-EFPS--LGK------L 317

Query: 92  PLYPSTTATIRTQGLAGITYI--ELSTLRKEKKTIFQIATERNQRAMITATPSGINYFIS 149
            +     ATIR  G+  +T I   +S L+       +       +++++     I +  S
Sbjct: 318 EILEEALATIRGYGI-RLTTICQSISQLK-------ETYGGEGAKSILSNHAVVICFAAS 369

Query: 150 NAENTSKKIS 159
           N E T+K IS
Sbjct: 370 NDEETAKYIS 379


>gnl|CDD|29736 cd01017, AdcA, Metal binding protein AcdA.  These proteins have
           been shown to function in the ABC uptake of Zn2+ and
           Mn2+ and in competence for genetic transformation and
           adhesion.  The AcdA proteins belong to the TroA
           superfamily of helical backbone metal receptor proteins
           that share a distinct fold and ligand binding mechanism.
            They are comprised of two globular subdomains connected
           by a long alpha helix and they bind their ligand in the
           cleft between these domains.  In addition, many of these
           proteins have a low complexity region containing metal
           binding histidine-rich motif (repetitive HDH sequence)..
          Length = 282

 Score = 27.5 bits (61), Expect = 7.2
 Identities = 9/36 (25%), Positives = 17/36 (47%), Gaps = 2/36 (5%)

Query: 329 ISTINTIENITSNLNDSSQKFAELMSKINNISALKE 364
           +  +N +E +T    D  + +  LM +  N+  LK 
Sbjct: 246 LLVLNPLETLTKEEIDDGKDYFSLMKE--NLETLKR 279


>gnl|CDD|153311 cd07627, BAR_Vps5p, The Bin/Amphiphysin/Rvs (BAR) domain of yeast
           Sorting Nexin Vps5p.  BAR domains are dimerization,
           lipid binding and curvature sensing modules found in
           many different proteins with diverse functions. Sorting
           nexins (SNXs) are Phox homology (PX) domain containing
           proteins that are involved in regulating membrane
           traffic and protein sorting in the endosomal system.
           SNXs differ from each other in their lipid-binding
           specificity, subcellular localization and specific
           function in the endocytic pathway. A subset of SNXs also
           contain BAR domains. The PX-BAR structural unit
           determines the specific membrane targeting of SNXs.
           Vsp5p is the yeast counterpart of human SNX1 and is part
           of the retromer complex, which functions in the
           endosome-to-Golgi retrieval of vacuolar protein sorting
           receptor Vps10p, the Golgi-resident membrane protein
           A-ALP, and endopeptidase Kex2. BAR domains form dimers
           that bind to membranes, induce membrane bending and
           curvature, and may also be involved in protein-protein
           interactions.
          Length = 216

 Score = 27.7 bits (62), Expect = 7.3
 Identities = 37/210 (17%), Positives = 74/210 (35%), Gaps = 45/210 (21%)

Query: 219 TITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQ--E 276
            +  L + L ++ K+++L                      ++ +   +  ET +     E
Sbjct: 12  YLDSLESQLKQLYKSLEL----------------VSSQRKELASATEEFAETLEALSSLE 55

Query: 277 VGQKIDHLLSDFSS-KMKSKETSAFLENIADSTSNMRS--------SISAIREITDQRQK 327
           + + +  LL+  +  + + KE+   LE  A                SI ++R    QRQK
Sbjct: 56  LSKSLSDLLAALAEVQKRIKES---LERQALQDVLTLGVTLDEYIRSIGSVRAAFAQRQK 112

Query: 328 IISTINTIENITSNLNDSSQKFAELMSKINNISA-LKENNSLFKDAQRAMHT----FRDT 382
           +     + E+    L+    +  +L  +       L    S  ++A+R        F + 
Sbjct: 113 LWQYWQSAES---ELSKKKAQLEKLKRQGKTQQEKLNSLLSELEEAERRASELKKEFEEV 169

Query: 383 SEKINRYIPSIGNNLQNFSQSGLNDIQNLV 412
           SE I          L+ F +  + D +N V
Sbjct: 170 SELIKS-------ELERFERERVEDFRNSV 192


>gnl|CDD|37518 KOG2307, KOG2307, KOG2307, Low density lipoprotein receptor
           [Intracellular trafficking, secretion, and vesicular
           transport].
          Length = 705

 Score = 27.6 bits (61), Expect = 7.8
 Identities = 26/146 (17%), Positives = 49/146 (33%), Gaps = 10/146 (6%)

Query: 272 QTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKIIST 331
               ++ Q ++ L  +  S   S   +              S + + RE   +   +I  
Sbjct: 89  DALNKIEQPLNQLREEIKSTRGSVGEAERALR------QQCSELCSNREKKIELLDLIYV 142

Query: 332 INTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRYIP 391
           +  IE ++  L     K  +  +      AL+ N   F  +      F  + E+I     
Sbjct: 143 LVAIEKLSKMLLSPPSKEQQDGATSLERIALELNQLKFHASHLKGSLFPHSEERIAAEKI 202

Query: 392 SIGNNLQNFSQSGLN----DIQNLVR 413
            +  +L      GL     D+QN +R
Sbjct: 203 ILSQSLAVLFAEGLQSAAGDLQNCLR 228


>gnl|CDD|29484 cd00386, Heme_Cu_Oxidase_III_like, Heme-copper oxidase subunit
          III.  Heme-copper oxidases are transmembrane protein
          complexes in the respiratory chains of prokaryotes and
          mitochondria which couple the reduction of molecular
          oxygen to water to, proton pumping across the membrane.
          The heme-copper oxidase superfamily is diverse in terms
          of electron donors, subunit composition, and heme
          types.  This superfamily includes cytochrome c and
          ubiquinol oxidases.  Bacterial oxidases typically
          contain 3 or 4 subunits in contrast to the 13 subunit
          bovine cytochrome c oxidase (CcO). Subunits I, II, and
          III of mammalian CcO are encoded within the
          mitochondrial genome and the remaining 10 subunits are
          encoded within the nuclear genome. Subunits I, II and
          III of ubiquinol oxidase are homologous to the
          corresponding subunits in CcO.  This group additionally
          contains proteins which are fusions between subunits I
          and III, such as Sulfolobus acidocaldarius SoxM, a
          subunit of the SoxM terminal oxidase complex. It also
          includes NorE which has been speculated to be a subunit
          of nitric oxide reductase. Some archaebacterial
          cytochrome oxidases lack subunit III.   Although not
          required for catalytic activity, subunit III is
          believed to play a role in assembly of the multimer
          complex. Rhodobacter CcO subunit III stabilizes the
          integrity of the binuclear center in subunit I.  It has
          been proposed that archaea acquired heme-copper
          oxidases through gene transfer from gram-positive
          bacteria..
          Length = 183

 Score = 27.5 bits (61), Expect = 8.0
 Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 2/43 (4%)

Query: 1  MESKNYYTSVGLFVVS--ILFFSFFSIYWLSRSNQYDGPMAEV 41
                   + LF++S  +LF SFF  Y+ SR +      A +
Sbjct: 4  SVRSGGRLGMWLFILSEVMLFGSFFWAYFHSRLSPPVEFGAGL 46


>gnl|CDD|32784 COG2964, COG2964, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 220

 Score = 27.5 bits (61), Expect = 8.1
 Identities = 23/149 (15%), Positives = 45/149 (30%), Gaps = 24/149 (16%)

Query: 278 GQKIDHLLSDFSSKM------KSKETSAFLENIADSTSNMRSSISAIREITDQRQKIIST 331
           G+++   ++D +  +        K         A     ++SS   IR   ++  +II  
Sbjct: 53  GRQVGSPITDLALDLLHNKEGSEKSVIGNYFTRAKDGRLIKSSSIFIR---NKEGRIIGM 109

Query: 332 INTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRYI- 390
           +  I    S L   S      M        +   N            F  + E +   + 
Sbjct: 110 L-CINMDLSLLVPVSAFLQTFMPTDETPKRVSSVN------------FASSVEDLVAQLL 156

Query: 391 -PSIGNNLQNFSQSGLNDIQNLVRKLQET 418
             +I     +   S     + +V+ L E 
Sbjct: 157 EWTIQEVNADRLLSNNAKNREIVKALYEK 185


>gnl|CDD|153293 cd07609, BAR_SIP3_fungi, The Bin/Amphiphysin/Rvs (BAR) domain of
           fungal Snf1p-interacting protein 3.  BAR domains are
           dimerization, lipid binding and curvature sensing
           modules found in many different proteins with diverse
           functions including organelle biogenesis, membrane
           trafficking or remodeling, and cell division and
           migration. This group is composed of mostly
           uncharacterized fungal proteins with similarity to
           Saccharomyces cerevisiae Snf1p-interacting protein 3
           (SIP3). These proteins contain an N-terminal BAR domain
           followed by a Pleckstrin Homology (PH) domain. SIP3
           interacts with SNF1 protein kinase and activates
           transcription when anchored to DNA. It may function in
           the SNF1 pathway. BAR domains form dimers that bind to
           membranes, induce membrane bending and curvature, and
           may also be involved in protein-protein interactions.
          Length = 214

 Score = 27.2 bits (61), Expect = 8.4
 Identities = 10/61 (16%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 240 NQILENIQVSSNNFVKSSDQVINTVHDV-RETTQTFQEVGQKIDHLLSDFSSKMKSKETS 298
             +L  ++ + +  +      + +     +E  + F+   +K D +L+ + ++ K+KE S
Sbjct: 77  GGVLSALKGNDSLILDPLRSFVKSDIRPYKELRKNFEYYQRKYDSMLARYVAQSKTKEPS 136

Query: 299 A 299
           +
Sbjct: 137 S 137


>gnl|CDD|35383 KOG0161, KOG0161, KOG0161, Myosin class II heavy chain
            [Cytoskeleton].
          Length = 1930

 Score = 27.1 bits (60), Expect = 9.2
 Identities = 35/212 (16%), Positives = 82/212 (38%), Gaps = 26/212 (12%)

Query: 228  DKMIKAID--LQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLL 285
            ++ ++A +  +QK+ + L+  +       +   +++   +D++E  Q  +E   + + LL
Sbjct: 837  EEEMRAKEEEIQKLKEELQKSESKRKELEEKLVKLLEEKNDLQEQLQAEKENLAEAEELL 896

Query: 286  SDFSSKMKS-----KETSAFLENI----ADSTSNMRSSISAIREITDQ-------RQKII 329
                ++ +      KE    LE      A+     R     ++E+ +Q        QK+ 
Sbjct: 897  ERLRAEKQELEKELKELKERLEEEEEKNAELERKKRKLEQEVQELKEQLEELELTLQKLE 956

Query: 330  STINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRY 389
               N  EN   NL +      E +SK++      E     ++ Q  +    + ++ +N+ 
Sbjct: 957  LEKNAAENKLKNLEEEINSLDENISKLSKEKKELEERI--RELQDDLQAEEEKAKSLNKA 1014

Query: 390  IPSIGNNLQNF------SQSGLNDIQNLVRKL 415
               +   L +        +    +++   RKL
Sbjct: 1015 KAKLEQQLDDLEVTLEREKRIRMELEKAKRKL 1046


>gnl|CDD|31758 COG1570, XseA, Exonuclease VII, large subunit [DNA replication,
           recombination, and repair].
          Length = 440

 Score = 27.2 bits (60), Expect = 9.7
 Identities = 20/155 (12%), Positives = 62/155 (40%), Gaps = 5/155 (3%)

Query: 277 VGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQ--RQKIISTINT 334
           VG + D  L+DF + +++   +A  E +   ++ +   +  ++    +  R+ +      
Sbjct: 232 VGHETDFTLADFVADLRAPTPTAAAELVVPDSAELLQQLDQLQRRLHRALRRLLDQKKQR 291

Query: 335 IENITSNL--NDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRYIPS 392
           +E++   L      +  +E   +++ + A++   +L              ++++N  I  
Sbjct: 292 LEHLARRLQFRSPERLLSEQQQRLDEL-AIRLRRALENQLALKKQRLERLTQRLNPQIQR 350

Query: 393 IGNNLQNFSQSGLNDIQNLVRKLQETVNHFDDCLN 427
               LQ   +     ++  +++ +E +    + L 
Sbjct: 351 QQQRLQQLERRLDKALRRQLKRKRERLEALVEQLE 385


  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
   0.314    0.129    0.350 

Gapped
Lambda     K      H
   0.267   0.0723    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,847,080
Number of extensions: 243456
Number of successful extensions: 976
Number of sequences better than 10.0: 1
Number of HSP's gapped: 972
Number of HSP's successfully gapped: 98
Length of query: 452
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 355
Effective length of database: 4,167,664
Effective search space: 1479520720
Effective search space used: 1479520720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.5 bits)