RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

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

Query= gi|254780858|ref|YP_003065271.1| NADH dehydrogenase I subunit F
[Candidatus Liberibacter asiaticus str. psy62]
         (425 letters)



>3i9v_1 NADH-quinone oxidoreductase subunit 1; electron transport,
           respiratory chain, 4Fe- 4S, cell membrane, flavoprotein,
           FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8}
           PDB: 2fug_1* 3iam_1* 3ias_1*
          Length = 438

 Score =  382 bits (983), Expect = e-107
 Identities = 189/422 (44%), Positives = 264/422 (62%), Gaps = 9/422 (2%)

Query: 5   QDRIFTNLYGLQGKSLSDSMSRGHWDNVDKIL-EKGRDWIINEVKASGLRGRGGAGFSTG 63
           +  ++ ++      +L   +  G ++   ++L EK  D +I EVK SGLRGRGGAGF TG
Sbjct: 14  ERTLYAHVGKEGSWTLDYYLRHGGYETAKRVLKEKTPDEVIEEVKRSGLRGRGGAGFPTG 73

Query: 64  MKWSFMPKVCSDRPHYLVVNADESEPGTCKDRDIMRHEPHTLIEGCVIASFAIGAHCAFI 123
           +KWSFMPK    + HYL+ NADESEPG+ KDR I+   PH LIEG ++A +AI A   +I
Sbjct: 74  LKWSFMPK-DDGKQHYLICNADESEPGSFKDRYILEDVPHLLIEGMILAGYAIRATVGYI 132

Query: 124 YVRGEFIRERESLQAAVDECYASGLLG-SNSKLGYDVDIIVHHGAGAYICGEETALLESL 182
           YVRGE+ R  + L+ A+ E  A G LG +     +  D+ VH GAGAYICGEETAL+ SL
Sbjct: 133 YVRGEYRRAADRLEQAIKEARARGYLGKNLFGTDFSFDLHVHRGAGAYICGEETALMNSL 192

Query: 183 EGKKGQPRLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENNRGTKLF 242
           EG +  PRLKPPFPA  GL+G PTT+NNVE++A V  I+ RGA W++  G E ++G KL+
Sbjct: 193 EGLRANPRLKPPFPAQSGLWGKPTTINNVETLASVVPIMERGADWFAQMGTEQSKGMKLY 252

Query: 243 SISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCLP-AGQMRGA 301
            ISG V  P   E  M  TF ELI +  GG     + + A+IPGGSS P LP   ++   
Sbjct: 253 QISGPVKRPGVYELPMGTTFRELIYEWAGGP---LEPIQAIIPGGSSTPPLPFTEEVLDT 309

Query: 302 IMDYDGLKEMGSGLGTAAVIVMDRSTDIIKAIWRLSVFYKHESCGQCTPCREGT-GWMMR 360
            M Y+ L+  GS LGT  VI++     ++ A+W L+ FY HESCG+CTPCREG  G+M+ 
Sbjct: 310 PMSYEHLQAKGSMLGTGGVILIPERVSMVDAMWNLTRFYAHESCGKCTPCREGVAGFMVN 369

Query: 361 VMERLVKGIAQKREIDLLYEVSKNIEGRTICALGDAAAWPIQGLIKNFRPLIEERIDQYH 420
           +  ++  G  ++++++ L  +   IEGR+ C L DAA WP++G +++F+        +  
Sbjct: 370 LFAKIGTGQGEEKDVENLEALLPLIEGRSFCPLADAAVWPVKGSLRHFKDQYLALARE-K 428

Query: 421 RC 422
           R 
Sbjct: 429 RP 430


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
           acyl-carrier-protein, beta-ketoacyl reductase,
           beta-ketoacyl synthase, dehydratase; 4.00A
           {Saccharomyces cerevisiae}
          Length = 2006

 Score = 61.5 bits (149), Expect = 4e-10
 Identities = 76/435 (17%), Positives = 121/435 (27%), Gaps = 199/435 (45%)

Query: 101 EPHTLIEGCVIASFAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSNSKLGYDVD 160
           EP T  E  ++  F +G + + +    +  +  + L   + E + +  L  N       D
Sbjct: 53  EPTTPAE--LVGKF-LG-YVSSLVEPSKVGQFDQVLNLCLTE-FENCYLEGN-------D 100

Query: 161 IIVHHGAGAYICGEETALLESLEGKK-------------GQPRLKPPFPANVGLYGCPTT 207
           I  H  A   +   +T L++     K              +P  K    A   L+     
Sbjct: 101 I--HALAAKLLQENDTTLVK----TKELIKNYITARIMAKRPFDKKSNSA---LF----- 146

Query: 208 VNNVESIAVVPTILRRGASWYSGFG------------RENNRGTKLFSISGHVNYPCTVE 255
              V             A   + FG            R+      L+       Y   V 
Sbjct: 147 -RAVGE---------GNAQLVAIFGGQGNTDDYFEELRD------LYQT-----YHVLVG 185

Query: 256 E---SMSITFDELI------EKHCGGIRG----GW----------DNLLAVIPGGSSVP- 291
           +     + T  ELI      EK     +G     W          D LL++ P   S P 
Sbjct: 186 DLIKFSAETLSELIRTTLDAEKVFT--QGLNILEWLENPSNTPDKDYLLSI-P--ISCPL 240

Query: 292 -CL----------------PAGQMRGAIMDYDGLKEMGS-----GLGTAAVIVMDRSTDI 329
             +                P G++R        LK  G+     GL TA  I    S   
Sbjct: 241 IGVIQLAHYVVTAKLLGFTP-GELR------SYLK--GATGHSQGLVTAVAIAETDS--- 288

Query: 330 IKAIWRLSVFYKHES------------CGQCTPCR--------------EGT-GWMMRV- 361
               W  S F+                C +  P                EG    M+ + 
Sbjct: 289 ----WE-S-FFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSIS 342

Query: 362 ---MERLVKGIAQ--------KR-EIDLLYEVSKNIEGRT--ICALGDAAAWPIQGL--- 404
               E++   + +        K+ EI L       + G    + + G   +  + GL   
Sbjct: 343 NLTQEQVQDYVNKTNSHLPAGKQVEISL-------VNGAKNLVVS-GPPQS--LYGLNLT 392

Query: 405 ---IKNFRPLIEERI 416
               K    L + RI
Sbjct: 393 LRKAKAPSGLDQSRI 407



 Score = 49.6 bits (118), Expect = 1e-06
 Identities = 71/488 (14%), Positives = 117/488 (23%), Gaps = 262/488 (53%)

Query: 3   TDQDRIFTNLYGLQG------------------------KSLSD---SMSRGHWDNVDKI 35
               ++   ++G QG                        K  ++    + R    + +K+
Sbjct: 151 EGNAQLVA-IFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTT-LDAEKV 208

Query: 36  LEKGRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVCSDR----------P-------- 77
             +G +  I                   ++W   P    D+          P        
Sbjct: 209 FTQGLN--I-------------------LEWLENPSNTPDKDYLLSIPISCPLIGVIQLA 247

Query: 78  HYLVVNADESEPGTCKDRDIMRHEP------------HT--LIEGCVIAS---------- 113
           HY+V         T K   ++   P            H+  L+    IA           
Sbjct: 248 HYVV---------TAK---LLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVS 295

Query: 114 --------FAIGAHCAFIYVR--------------GEF-------IR--ERESLQAAVDE 142
                   F IG  C   Y                 E        I    +E +Q  V++
Sbjct: 296 VRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNK 355

Query: 143 CYASGLLGSNSKLGYD--VDIIVHHGAGAYICGEETALLESLEG------------KKGQ 188
                    NS L     V+I + +GA   +    +   +SL G               Q
Sbjct: 356 T--------NSHLPAGKQVEISLVNGAKNLVV---SGPPQSLYGLNLTLRKAKAPSGLDQ 404

Query: 189 PRL-----KPPFPANVGLYGCPTTVNNVESIAV----------VPTILRR----GASW-- 227
            R+     K  F             N    +A              I +       S+  
Sbjct: 405 SRIPFSERKLKF------------SNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNA 452

Query: 228 -------YSGFGRENNR--GTKLFS------ISGHVNYPCTVEESMS--ITFDELIEKHC 270
                  Y  F   + R     +        I   V +  T +   +  + F        
Sbjct: 453 KDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFG------- 505

Query: 271 GGIRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGL-------KEMGSGLGTAAVIV- 322
                         PGG+S                 GL       K+ G+G+    VIV 
Sbjct: 506 --------------PGGAS-----------------GLGVLTHRNKD-GTGV---RVIVA 530

Query: 323 --MDRSTD 328
             +D + D
Sbjct: 531 GTLDINPD 538



 Score = 29.1 bits (65), Expect = 1.7
 Identities = 40/190 (21%), Positives = 78/190 (41%), Gaps = 28/190 (14%)

Query: 240  KLF-SISGH-VNYPCTVEESM--SITFDE----LIEKHCGGIRGGWDNLLA--VIPGGSS 289
            K+F  I+ H  +Y    E+ +  +  F +    L+EK        +++L +  +IP  ++
Sbjct: 1705 KIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEK------AAFEDLKSKGLIPADAT 1758

Query: 290  VPCLPAGQMRGAIMDYDGLKEMGSGLGTAAVI--VMDRSTDIIKAIWRLSVFYKHESCGQ 347
                 AG   G   +Y  L  +   +   +++  V  R   +  A+ R  +   +     
Sbjct: 1759 F----AGHSLG---EYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIA 1811

Query: 348  CTPCREGTGWMMRVMERLVKGIAQKREIDLLYEVSKNIEGRTICALGDAAAWPIQGLIKN 407
              P R    +    ++ +V+ +  KR   L+  V+ N+E +   A GD  A      + N
Sbjct: 1812 INPGRVAASFSQEALQYVVERVG-KRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLN 1870

Query: 408  FRPLIEERID 417
            F  L  ++ID
Sbjct: 1871 FIKL--QKID 1878


>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
            acid synthase, acyl-carrier-protein, beta-ketoacyl
            reductase, beta-ketoacyl synthase, dehydratase; 4.00A
            {Saccharomyces cerevisiae}
          Length = 1688

 Score = 29.4 bits (65), Expect = 1.7
 Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 4/39 (10%)

Query: 30   DNVDKILEKGRDWII---NEVKASGLRGRGGAGFSTGMK 65
            DNVDKILE+  ++++     +K  G+R      F  G K
Sbjct: 1413 DNVDKILEQ-FEYVLYPSKTLKTDGVRAVSITSFGFGQK 1450


>1zx5_A Mannosephosphate isomerase, putative; structural genomics, PSI,
           protein structure initiative, midwest center for
           structural genomics, MCSG; HET: LFR; 2.30A
           {Archaeoglobus fulgidus} SCOP: b.82.1.3
          Length = 300

 Score = 28.5 bits (63), Expect = 3.1
 Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 1/46 (2%)

Query: 231 FGRENNRGTKLFSISGHVNYPCTVEES-MSITFDELIEKHCGGIRG 275
            G   +   + +  S H + P TV      ++  EL  KH   + G
Sbjct: 29  KGFRQSGIGESWEFSAHTSRPSTVLVKGQQLSMIELFSKHRDELLG 74


>1zb7_A Neurotoxin; hexxh metalloprotease; HET: FLC; 2.35A {Clostridium
           botulinum}
          Length = 455

 Score = 27.1 bits (60), Expect = 7.0
 Identities = 7/45 (15%), Positives = 12/45 (26%), Gaps = 6/45 (13%)

Query: 317 TAAVIVMDRSTDIIKAIWRLSVFYKHESCGQCTPCREGTGWMMRV 361
              +I+      +        +   H       P  EG G  M +
Sbjct: 155 MTNLIIFGPGPVLSDNFTDSMIMNGHS------PISEGFGARMMI 193


  Database: pdb70
    Posted date:  Jan 26, 2011 11:21 AM
  Number of letters in database: 5,693,230
  Number of sequences in database:  24,244
  
Lambda     K      H
   0.321    0.139    0.437 

Gapped
Lambda     K      H
   0.267   0.0593    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 3,913,135
Number of extensions: 187992
Number of successful extensions: 465
Number of sequences better than 10.0: 1
Number of HSP's gapped: 457
Number of HSP's successfully gapped: 9
Length of query: 425
Length of database: 5,693,230
Length adjustment: 95
Effective length of query: 330
Effective length of database: 3,390,050
Effective search space: 1118716500
Effective search space used: 1118716500
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 (21.8 bits)
S2: 58 (26.4 bits)