RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254781086|ref|YP_003065499.1| F0F1 ATP synthase subunit B'
[Candidatus Liberibacter asiaticus str. psy62]
         (176 letters)



>gnl|CDD|169692 PRK09174, PRK09174, F0F1 ATP synthase subunit B'; Validated.
          Length = 204

 Score =  120 bits (302), Expect = 2e-28
 Identities = 58/151 (38%), Positives = 84/151 (55%), Gaps = 1/151 (0%)

Query: 13  FPPFDTSTFLSQFFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREV 72
           FPPFD++ + SQ  WLAI FG+FY    R ILPR+  I+E RR+ I+ D ++    K+E 
Sbjct: 44  FPPFDSTHYASQLLWLAITFGLFYLFMSRVILPRIGGIIETRRDRIAQDLDQAARLKQEA 103

Query: 73  ESMISSYEESLAIARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLSNAQNEIDDMQK 132
           ++ +++YE+ LA ARA A  I      AA+   E +R   E  L  KL  A+  I  ++ 
Sbjct: 104 DAAVAAYEQELAQARAKAHSIAQAAREAAKAKAEAERAAIEASLEKKLKEAEARIAAIKA 163

Query: 133 KASQEVYSIVGEVTKDLVRKL-GFSVSDADV 162
           KA  +V SI  E    +V +L G +   A V
Sbjct: 164 KAMADVGSIAEETAAAIVEQLIGGTADKASV 194


>gnl|CDD|184061 PRK13454, PRK13454, F0F1 ATP synthase subunit B'; Provisional.
          Length = 181

 Score = 72.9 bits (179), Expect = 4e-14
 Identities = 40/163 (24%), Positives = 78/163 (47%)

Query: 10  SSRFPPFDTSTFLSQFFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAK 69
           +   P  D STF +Q FWL +     Y+V  R  LPR+ +++  R+  I++D    +  K
Sbjct: 19  APGMPQLDFSTFPNQIFWLLVTLVAIYFVLTRVALPRIGAVLAERQGTITNDLAAAEELK 78

Query: 70  REVESMISSYEESLAIARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLSNAQNEIDD 129
           ++      +Y ++LA ARA A+ I+ +  A  +  L+      + ++  K + ++  I +
Sbjct: 79  QKAVEAEKAYNKALADARAEAQRIVAETRAEIQAELDVAIAKADAEIAAKAAESEKRIAE 138

Query: 130 MQKKASQEVYSIVGEVTKDLVRKLGFSVSDADVQKILDRKRDG 172
           ++  A + V  +  +  + LV  LG     A V   + ++  G
Sbjct: 139 IRAGALESVEEVAKDTAEALVAALGGKADAAAVDAAVAQRMKG 181


>gnl|CDD|180240 PRK05759, PRK05759, F0F1 ATP synthase subunit B; Validated.
          Length = 156

 Score = 67.5 bits (166), Expect = 2e-12
 Identities = 41/145 (28%), Positives = 68/145 (46%), Gaps = 1/145 (0%)

Query: 25  FFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEESLA 84
                I F I  W   +F+ P +   +E R+  I+      + AK+E+E   + YE  LA
Sbjct: 7   LIGQLIAFLILVWFIMKFVWPPIMKALEERQKKIADGLAAAERAKKELELAQAKYEAQLA 66

Query: 85  IARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLSNAQNEIDDMQKKASQEVYSIVGE 144
            ARA A EII++    A Q +E  +   E +     + AQ EI+  +K+A +E+   V +
Sbjct: 67  EARAEAAEIIEQAKKRAAQIIEEAKAEAEAEAARIKAQAQAEIEQERKRAREELRKQVAD 126

Query: 145 VTKDLVRK-LGFSVSDADVQKILDR 168
           +      K LG  +  A    ++D+
Sbjct: 127 LAVAGAEKILGRELDAAAQSDLIDK 151


>gnl|CDD|180627 PRK06569, PRK06569, F0F1 ATP synthase subunit B'; Validated.
          Length = 155

 Score = 56.0 bits (135), Expect = 5e-09
 Identities = 38/124 (30%), Positives = 64/124 (51%), Gaps = 5/124 (4%)

Query: 14  PPFDTSTFLSQFFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREVE 73
           P FD +T+ SQ FWL + FG+ Y   ++FI P+   I   R+  I  +  + D+   EVE
Sbjct: 2   PQFDIATYYSQIFWLIVTFGLLYIFVYKFITPKAEEIFNNRQTNIQDNITQADTLTIEVE 61

Query: 74  SMISSYEESLAIARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLSNAQNE-IDDMQK 132
            +   Y E   I + + +  ID++      +LE +  + +K+L   L N+ N+ I+D+  
Sbjct: 62  KLNKYYNE--EIDKTNTE--IDRLKKEKIDSLESEFLIKKKNLEQDLKNSINQNIEDINL 117

Query: 133 KASQ 136
            A Q
Sbjct: 118 AAKQ 121


>gnl|CDD|172947 PRK14472, PRK14472, F0F1 ATP synthase subunit B; Provisional.
          Length = 175

 Score = 40.9 bits (96), Expect = 2e-04
 Identities = 39/142 (27%), Positives = 68/142 (47%), Gaps = 6/142 (4%)

Query: 26  FWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEESLAI 85
           FW A+ F I   +  +     + S +E R   I S  ++  SAK E E+++    E LA 
Sbjct: 22  FWTAVTFVIVLLILKKIAWGPILSALEEREKGIQSSIDRAHSAKDEAEAILRKNRELLAK 81

Query: 86  ARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHK---LSNAQNEIDDMQKKASQEVYSIV 142
           A A A +II +    AE+    + E+ EK        +++A+ EI+  +++A   + + V
Sbjct: 82  ADAEADKIIREGKEYAEK---LRAEITEKAHTEAKKMIASAKEEIEQEKRRALDVLRNEV 138

Query: 143 GEVTKDLVRKLGFSVSDADVQK 164
            ++      K+  +  DAD QK
Sbjct: 139 ADLAVKGAEKIIRTSLDADKQK 160


>gnl|CDD|130214 TIGR01144, ATP_synt_b, ATP synthase, F0 subunit b.  This model
           describes the F1/F0 ATP synthase b subunit in bacteria
           only. Scoring just below the trusted cutoff are the
           N-terminal domains of Mycobacterial b/delta fusion
           proteins and a subunit from an archaeon, Methanosarcina
           barkeri, in which the ATP synthase homolog differs in
           architecture and is not experimentally confirmed. This
           model helps resolve b from the related b' subunit.
           Within the family is an example from a
           sodium-translocating rather than proton-translocating
           ATP synthase.
          Length = 147

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 27/141 (19%), Positives = 63/141 (44%), Gaps = 1/141 (0%)

Query: 29  AIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEESLAIARA 88
            I F +  W   +++ P L+  +E R+  I+      + AK+E        +  L  A+ 
Sbjct: 2   LISFILLVWFCMKYVWPPLAKAIETRQKKIADGLASAERAKKEAALAQKKAQVILKEAKD 61

Query: 89  HAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLSNAQNEIDDMQKKASQEVYSIVGEVTKD 148
            A+EII+       + LE  +    ++     + A+ EI+  +++A +E+   V +++  
Sbjct: 62  EAQEIIENANKRGSEILEEAKAEAREEREKIKAQARAEIEAEKEQAREELRKQVADLSVL 121

Query: 149 LVRK-LGFSVSDADVQKILDR 168
              K +  ++     + ++D+
Sbjct: 122 GAEKIIERNIDKQAQKDLIDK 142


>gnl|CDD|179009 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
           protein; Reviewed.
          Length = 782

 Score = 35.6 bits (83), Expect = 0.007
 Identities = 20/92 (21%), Positives = 39/92 (42%), Gaps = 9/92 (9%)

Query: 56  NLISSDQEKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQNLEFQREVFEKD 115
           N+I   ++ +   K ++  +I+S EE        A+E          + L  + E  +++
Sbjct: 502 NIIEEAKKLIGEDKEKLNELIASLEELERELEQKAEEA---------EALLKEAEKLKEE 552

Query: 116 LLHKLSNAQNEIDDMQKKASQEVYSIVGEVTK 147
           L  K    Q E D + ++A +E    + E  K
Sbjct: 553 LEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKK 584


>gnl|CDD|184696 PRK14474, PRK14474, F0F1 ATP synthase subunit B; Provisional.
          Length = 250

 Score = 35.6 bits (82), Expect = 0.007
 Identities = 28/131 (21%), Positives = 57/131 (43%), Gaps = 14/131 (10%)

Query: 30  IIFGIFYWVTHRFILPRLSSIMEVRRNLISS---DQEKMD-SAKREVES---MISSYEES 82
           I F I  ++  RF+   +  +M+ R+  I++   D E+    A +E E       S E+ 
Sbjct: 13  INFLILVYLLRRFLYKPIIQVMKKRQQRIANRWQDAEQRQQEAGQEAERYRQKQQSLEQQ 72

Query: 83  ----LAIARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLSNAQNEIDDMQKKASQEV 138
               +A A+  A E    ++  A +++   R+ + + L  +    Q     +Q++  Q++
Sbjct: 73  RASFMAQAQEAADEQRQHLLNEAREDVATARDEWLEQLERE---KQEFFKALQQQTGQQM 129

Query: 139 YSIVGEVTKDL 149
             I+     DL
Sbjct: 130 VKIIRAALADL 140


>gnl|CDD|184695 PRK14471, PRK14471, F0F1 ATP synthase subunit B; Provisional.
          Length = 164

 Score = 34.4 bits (79), Expect = 0.015
 Identities = 28/136 (20%), Positives = 64/136 (47%), Gaps = 14/136 (10%)

Query: 25  FFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEESLA 84
           FFW  I+F I   +  +F    +   ++ R + I +     + A++E++++ +  E  L 
Sbjct: 11  FFWQTILFLILLLLLAKFAWKPILGAVKEREDSIKNALASAEEARKEMQNLQADNERLLK 70

Query: 85  IARAH-------AKEIIDKVVAAAEQNLEFQREVFEKDLLHKLSNAQNEIDDMQKKASQE 137
            ARA        A+EI +K++A A++  + + +   +        A+  I+  +  A  E
Sbjct: 71  EARAERDAILKEAREIKEKMIADAKEEAQVEGDKMIEQ-------AKASIESEKNAAMAE 123

Query: 138 VYSIVGEVTKDLVRKL 153
           + + V  ++ ++  K+
Sbjct: 124 IKNQVANLSVEIAEKV 139


>gnl|CDD|184064 PRK13461, PRK13461, F0F1 ATP synthase subunit B; Provisional.
          Length = 159

 Score = 34.6 bits (80), Expect = 0.015
 Identities = 22/117 (18%), Positives = 51/117 (43%)

Query: 22  LSQFFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEE 81
           +       I F I   +   F   ++ ++++ R++ I +  EK D  +++   +    E 
Sbjct: 5   IPTIIATIINFIILLLILKHFFFDKIKAVIDSRQSEIDNKIEKADEDQKKARELKLKNER 64

Query: 82  SLAIARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLSNAQNEIDDMQKKASQEV 138
            L  A+   K+I+++  + AE   E   +   ++    +  A+ E    ++KA  E+
Sbjct: 65  ELKNAKEEGKKIVEEYKSKAENVYEEIVKEAHEEADLIIERAKLEAQREKEKAEYEI 121


>gnl|CDD|132364 TIGR03321, alt_F1F0_F0_B, alternate F1F0 ATPase, F0 subunit B.  CC
           and in principle may run in either direction. This model
           represents the F0 subunit B of this apparent second ATP
           synthase.
          Length = 246

 Score = 33.5 bits (77), Expect = 0.032
 Identities = 33/150 (22%), Positives = 60/150 (40%), Gaps = 26/150 (17%)

Query: 15  PFDTSTFLSQFFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREVES 74
             D  T ++Q     I F I  W+  RF+   +   M+ R   I+ +    D+ KRE E 
Sbjct: 2   LIDWFTVIAQ----LINFLILVWLLKRFLYRPILDAMDAREKKIAGELADADTKKREAEQ 57

Query: 75  MISSYEESLAI---------------ARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHK 119
               YEE                   A+A  + ++D+    A++  E  +E   ++    
Sbjct: 58  ERREYEEKNEELDQQREVLLTKAKEEAQAERQRLLDEAREEADEIREKWQEALRRE---- 113

Query: 120 LSNAQNEIDDMQKKASQEVYSIVGEVTKDL 149
                   D+++++   EV++I  +V  DL
Sbjct: 114 ---QAALSDELRRRTGAEVFAIARKVLTDL 140


>gnl|CDD|181441 PRK08475, PRK08475, F0F1 ATP synthase subunit B; Validated.
          Length = 167

 Score = 32.7 bits (75), Expect = 0.060
 Identities = 36/165 (21%), Positives = 62/165 (37%), Gaps = 27/165 (16%)

Query: 17  DTSTFLSQFFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSD----QEKMDSAKREV 72
             +T         I F IF  +   F    L +  + R N IS      QEK+  +K + 
Sbjct: 17  LGATEQYDIIERTINFLIFVGILWYFAAKPLKNFYKSRINKISKRLEEIQEKLKESKEKK 76

Query: 73  ESMISSYEESLAIARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLSNAQNEIDDMQK 132
           E  +   EE        AKE  + +V  A++      +  EK         +++I+++ K
Sbjct: 77  EDALKKLEE--------AKEKAELIVETAKKEAYILTQKIEKQ-------TKDDIENLIK 121

Query: 133 --KASQE------VYSIVGEVTKDLVRKLGFSVSDADVQKILDRK 169
             +   E         +V EV  +L      S++  +   IL +K
Sbjct: 122 SFEELMEFEVRKMEREVVEEVLNELFESKKVSLNQQEYVNILLKK 166



 Score = 26.1 bits (58), Expect = 5.0
 Identities = 12/65 (18%), Positives = 32/65 (49%), Gaps = 7/65 (10%)

Query: 61  DQEKMDSAKREVESMISSYEESL-----AIARAHAKEIIDKVVAAAEQNLEFQREVFEKD 115
            Q+     K ++E++I S+EE +      + R   +E+++++     + +   ++ +   
Sbjct: 105 TQKIEKQTKDDIENLIKSFEELMEFEVRKMEREVVEEVLNELF--ESKKVSLNQQEYVNI 162

Query: 116 LLHKL 120
           LL K+
Sbjct: 163 LLKKV 167


>gnl|CDD|181442 PRK08476, PRK08476, F0F1 ATP synthase subunit B'; Validated.
          Length = 141

 Score = 32.4 bits (74), Expect = 0.070
 Identities = 22/107 (20%), Positives = 45/107 (42%), Gaps = 4/107 (3%)

Query: 29  AIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEESLAIARA 88
            ++F +   + + ++   L   M+ R   I +D EK+ +   +V  +    E  L  AR 
Sbjct: 14  FVVFLLLIVILNSWLYKPLLKFMDNRNASIKNDLEKVKTNSSDVSEIEHEIETILKNARE 73

Query: 89  HAKEIIDKVVAAA----EQNLEFQREVFEKDLLHKLSNAQNEIDDMQ 131
            A +I  K +A A    E+ +E ++   E           N+  +++
Sbjct: 74  EANKIRQKAIAKAKEEAEKKIEAKKAELESKYEAFAKQLANQKQELK 120


>gnl|CDD|180941 PRK07352, PRK07352, F0F1 ATP synthase subunit B; Validated.
          Length = 174

 Score = 32.2 bits (74), Expect = 0.077
 Identities = 28/137 (20%), Positives = 57/137 (41%), Gaps = 20/137 (14%)

Query: 2   ASSSSSDFSSRFPPFDTSTFLSQFFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSD 61
           A+ +   F       +T+        LAI+ G+ Y+    F    L  I+E RR  I   
Sbjct: 8   ATEAEGGFGLNLNLLETN-----LINLAIVIGLLYYFGRGF----LGKILEERREAILQA 58

Query: 62  QEKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLS 121
            ++ +   R+    ++  ++ LA A+  A    +++ A A+   E  R   EK       
Sbjct: 59  LKEAEERLRQAAQALAEAQQKLAQAQQEA----ERIRADAKARAEAIRAEIEK------- 107

Query: 122 NAQNEIDDMQKKASQEV 138
            A  ++  +++ A+ ++
Sbjct: 108 QAIEDMARLKQTAAADL 124


>gnl|CDD|179777 PRK04194, PRK04194, hypothetical protein; Provisional.
          Length = 392

 Score = 31.3 bits (72), Expect = 0.15
 Identities = 18/88 (20%), Positives = 32/88 (36%), Gaps = 12/88 (13%)

Query: 29  AIIF------GIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEES 82
            I+F      G+  +   R++L R    +E     +       D     + ++   YE+ 
Sbjct: 308 RILFRETGTLGVREYPVERWVLERRIETVETPYGEVRVKVAYRDG---GIINVKPEYEDC 364

Query: 83  LAIARAH---AKEIIDKVVAAAEQNLEF 107
             IAR      +E+      AAE+   F
Sbjct: 365 KRIARETGIPLREVYRAAEEAAEEFYAF 392


>gnl|CDD|139585 PRK13460, PRK13460, F0F1 ATP synthase subunit B; Provisional.
          Length = 173

 Score = 31.1 bits (70), Expect = 0.15
 Identities = 15/70 (21%), Positives = 31/70 (44%)

Query: 27 WLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEESLAIA 86
          W  + F +   V  +F    +   ++ R + + +D  K    + E E+++  YE  L  A
Sbjct: 21 WTLVTFLVVVLVLKKFAWDVILKALDERASGVQNDINKASELRLEAEALLKDYEARLNSA 80

Query: 87 RAHAKEIIDK 96
          +  A  I+ +
Sbjct: 81 KDEANAIVAE 90


>gnl|CDD|179887 PRK04863, mukB, cell division protein MukB; Provisional.
          Length = 1486

 Score = 30.7 bits (70), Expect = 0.20
 Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 11/92 (11%)

Query: 45  PRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQN 104
             L+ +    R      QEK++  + ++E +    EE        A E  ++  A AE  
Sbjct: 335 DHLNLVQTALRQ-----QEKIERYQADLEELEERLEEQ-NEVVEEADEQQEENEARAEAA 388

Query: 105 LEFQREVFEKDLLHKLSNAQNEIDDMQKKASQ 136
              + EV   +L  +L++ Q  +D  Q +A Q
Sbjct: 389 ---EEEV--DELKSQLADYQQALDVQQTRAIQ 415


>gnl|CDD|168615 PRK06568, PRK06568, F0F1 ATP synthase subunit B; Validated.
          Length = 154

 Score = 30.6 bits (69), Expect = 0.23
 Identities = 31/121 (25%), Positives = 61/121 (50%), Gaps = 6/121 (4%)

Query: 21  FLSQFFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYE 80
           FL + FWLA+ F IF ++ +R   P   +I+      I   QEK+  A++  E     +E
Sbjct: 3   FLDESFWLAVSFVIFVYLIYR---PAKKAILNSLDAKILEVQEKVLKAEKLKEDAALLFE 59

Query: 81  ESLAIAR---AHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLSNAQNEIDDMQKKASQE 137
           ++ A  +       ++I++     ++ ++ + +  E+ L HK S+A   I + +  AS+E
Sbjct: 60  QTNAQIKKLETLRSQMIEESNEVTKKIIQEKTKEIEEFLEHKKSDAIQLIQNQKSTASKE 119

Query: 138 V 138
           +
Sbjct: 120 L 120


>gnl|CDD|147793 pfam05832, DUF846, Eukaryotic protein of unknown function (DUF846).
            This family consists of several of unknown function
           from a variety of eukaryotic organisms.
          Length = 140

 Score = 30.3 bits (69), Expect = 0.26
 Identities = 13/30 (43%), Positives = 16/30 (53%)

Query: 9   FSSRFPPFDTSTFLSQFFWLAIIFGIFYWV 38
           F SR PPF  +   S  FWLA+     +WV
Sbjct: 76  FESRDPPFVPNAIDSNLFWLALYVAPLFWV 105


>gnl|CDD|179944 PRK05134, PRK05134, bifunctional 3-demethylubiquinone-9
           3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol
           methylase; Provisional.
          Length = 233

 Score = 30.1 bits (69), Expect = 0.34
 Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 3/36 (8%)

Query: 80  EESLAIARAHAKE---IIDKVVAAAEQNLEFQREVF 112
           EE++ +AR HA E    ID     AE+        F
Sbjct: 80  EENIEVARLHALESGLKIDYRQTTAEELAAEHPGQF 115


>gnl|CDD|179408 PRK02292, PRK02292, V-type ATP synthase subunit E; Provisional.
          Length = 188

 Score = 30.0 bits (68), Expect = 0.39
 Identities = 31/104 (29%), Positives = 53/104 (50%), Gaps = 20/104 (19%)

Query: 80  EESLAIARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLS-----------NAQNEI- 127
           EE +A A A A+EI++   A AE+ +E  RE        +LS           NA+ E+ 
Sbjct: 30  EEIIAEAEADAEEILEDREAEAEREIEQLRE-------QELSSAKLEAKRERLNARKEVL 82

Query: 128 DDMQKKASQEVYSIVGEVTKDLVRKLGFSVSDADVQKILDRKRD 171
           +D++ +   E+ S+ G+  ++L + L    +DAD  ++  RK D
Sbjct: 83  EDVRNQVEDEIASLDGDKREELTKSL-LDAADADGVRVYSRKDD 125


>gnl|CDD|132225 TIGR03181, PDH_E1_alph_x, pyruvate dehydrogenase E1 component,
           alpha subunit.  Members of this protein family are the
           alpha subunit of the E1 component of pyruvate
           dehydrogenase (PDH). This model represents one branch of
           a larger family that E1-alpha proteins from
           2-oxoisovalerate dehydrogenase, acetoin dehydrogenase,
           another PDH clade, etc.
          Length = 341

 Score = 29.4 bits (67), Expect = 0.46
 Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 4/70 (5%)

Query: 44  LPRLSSIMEVRRNLISSDQEKMDSAKREVESMIS-SYEESLAIARAHAKEIIDKVVAAAE 102
           + RL   +E R+ L   +QE  ++ + E E+ ++ +  E+LA+      +I D V A   
Sbjct: 275 ILRLRKYLE-RKGLWDEEQE--EALEEEAEAEVAEAVAEALALPPPPVDDIFDHVYAELP 331

Query: 103 QNLEFQREVF 112
             LE QR   
Sbjct: 332 PELEEQRAEL 341


>gnl|CDD|183147 PRK11465, PRK11465, putative mechanosensitive channel protein;
           Provisional.
          Length = 741

 Score = 29.4 bits (66), Expect = 0.47
 Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 3/34 (8%)

Query: 15  PFDTSTF---LSQFFWLAIIFGIFYWVTHRFILP 45
           PF+  TF   L+ F  LA++   FYW+     LP
Sbjct: 128 PFNPQTFSNALTHFLMLAVLVFGFYWLIRLCALP 161


>gnl|CDD|168917 PRK07353, PRK07353, F0F1 ATP synthase subunit B'; Validated.
          Length = 140

 Score = 29.2 bits (66), Expect = 0.59
 Identities = 21/99 (21%), Positives = 46/99 (46%), Gaps = 4/99 (4%)

Query: 55  RNLISSDQEKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQNLEFQREVFEK 114
           R   +  +E++     E E + + YE+ LA AR  A+ +I +  A A++         + 
Sbjct: 42  RTNRAEAKERLA----EAEKLEAQYEQQLASARKQAQAVIAEAEAEADKLAAEALAEAQA 97

Query: 115 DLLHKLSNAQNEIDDMQKKASQEVYSIVGEVTKDLVRKL 153
           +       A+ EI+  ++ A  ++   V  +++ ++ KL
Sbjct: 98  EAQASKEKARREIEQQKQAALAQLEQQVDALSRQILEKL 136


>gnl|CDD|163537 TIGR03825, FliH_bacil, flagellar assembly protein FliH.  This
           bacillus clade of FliH proteins is not found by the Pfam
           FliH model pfam02108, but is closely related to the
           sequences identified by that model. Sequences identified
           by this model are observed in flagellar operons in an
           analogous position relative to other flagellar operon
           genes.
          Length = 255

 Score = 29.0 bits (65), Expect = 0.61
 Identities = 24/100 (24%), Positives = 42/100 (42%), Gaps = 9/100 (9%)

Query: 41  RFILPRLSSIMEVRRNLISSDQ-EKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVA 99
             I    S I    R +I   Q   +   ++E+      +E+ L  A A A +II++   
Sbjct: 3   NIIKSTKSVIPAQERGIIPLRQVTDVPETEQELADEEQEFEQILEKAEAEAAQIIEQ--- 59

Query: 100 AAEQNLEFQREVFEKDLLHKLSNAQNEIDDMQKKASQEVY 139
            AE      RE  E+    + +  + E + + ++A QE Y
Sbjct: 60  -AEAQAAAIREQIEQ----ERAQWEEERERLIQEAKQEGY 94


>gnl|CDD|148840 pfam07464, ApoLp-III, Apolipophorin-III precursor (apoLp-III).
           This family consists of several insect
           apolipoprotein-III sequences. Exchangeable
           apolipoproteins constitute a functionally important
           family of proteins that play critical roles in lipid
           transport and lipoprotein metabolism. Apolipophorin III
           (apoLp-III) is a prototypical exchangeable
           apolipoprotein found in many insect species that
           functions in transport of diacylglycerol (DAG) from the
           fat body lipid storage depot to flight muscles in the
           adult life stage.
          Length = 166

 Score = 28.7 bits (64), Expect = 0.78
 Identities = 25/102 (24%), Positives = 43/102 (42%), Gaps = 14/102 (13%)

Query: 62  QEKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLS 121
           +E  D   ++++++ +S +E+L  A   AKE     +    QN+E   E   K       
Sbjct: 44  KEGSDKVLQQLKALSASLQEALKDANGKAKE----ALEQLRQNIEETAEELRKAHPEVEQ 99

Query: 122 NAQNEIDDMQ----------KKASQEVYSIVGEVTKDLVRKL 153
            AQ   D +Q          +K ++EV S V    + L  K+
Sbjct: 100 QAQELRDKLQAAVQSTVQESQKLAKEVASNVEGTNEKLAPKI 141


>gnl|CDD|150104 pfam09325, Vps5, Vps5 C terminal like.  Vps5 is a sorting nexin
           that functions in membrane trafficking. This is the C
           terminal dimerization domain.
          Length = 236

 Score = 28.0 bits (63), Expect = 1.4
 Identities = 20/99 (20%), Positives = 37/99 (37%), Gaps = 8/99 (8%)

Query: 46  RLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEESLAIARA--HAKEIIDKVVAAAEQ 103
            LS + EV   +    + +       +   I  Y   +   +A  + +    +    AEQ
Sbjct: 83  ALSQLAEVEERIKELLERQALQDVLTLGETIDEYLRLIGSVKAVFNQRVKAWQQWQNAEQ 142

Query: 104 NLEFQREVFEKDLL------HKLSNAQNEIDDMQKKASQ 136
           +L  +R    K          KL  A+ E+D+ ++K  Q
Sbjct: 143 DLSKKRAQLAKLKGAGKSRQDKLQQAKKEVDEAERKVQQ 181


>gnl|CDD|152163 pfam11727, ISG65-75, Invariant surface glycoprotein.  This family
           is found in Trypanosome species, and appears to be one
           of two invariant surface glycoproteins, ISG65 and ISG75.
           that are found in the mammalian stage of the parasitic
           protozoan. the sequence suggests the two families are
           polypeptides with N-terminal signal sequences,
           hydrophilic extracellular domains, single trans-membrane
           alpha-helices and short cytoplasmic domains. they are
           both expressed in the bloodstream form but not in the
           midgut stage. Both polypeptides are distributed over the
           entire surface of the parasite.
          Length = 289

 Score = 27.9 bits (62), Expect = 1.6
 Identities = 14/69 (20%), Positives = 29/69 (42%), Gaps = 2/69 (2%)

Query: 56  NLISSDQEKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQNLEFQREVFEKD 115
            L  SD++K+     + +  I         A   A+++ ++V  AA + L +  +    +
Sbjct: 95  KLSDSDKKKIKEICEKAKDKIDEALPEAKKAGREAEKLAEEVKEAAAKALGWALDEGTSN 154

Query: 116 --LLHKLSN 122
              L K+ N
Sbjct: 155 STGLSKVLN 163


>gnl|CDD|151530 pfam11085, YqhR, Conserved membrane protein YqhR.  This family is
           conserved in the Bacillaceae family of the Firmicutes.
           The function is not known.
          Length = 174

 Score = 27.7 bits (62), Expect = 1.7
 Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 6/45 (13%)

Query: 20  TFLSQFF--WLAIIFGIFYWVTHRFIL----PRLSSIMEVRRNLI 58
             L +    W  I++G+  W+   F+L    P +  + E+ +N I
Sbjct: 91  ALLKKVKSMWPGILYGLALWLLVFFVLNPIFPDVKPVTELDKNTI 135


>gnl|CDD|179204 PRK01005, PRK01005, V-type ATP synthase subunit E; Provisional.
          Length = 207

 Score = 27.4 bits (61), Expect = 1.9
 Identities = 12/54 (22%), Positives = 28/54 (51%)

Query: 63  EKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQNLEFQREVFEKDL 116
           E +  A+ E  +++ + +E      A A+E  +K++ +AE+  + + +  E  L
Sbjct: 20  ETLKPAEEEAGAIVHNAKEQAKRIIAEAQEEAEKIIRSAEETADQKLKQGESAL 73


>gnl|CDD|184510 PRK14105, PRK14105, selenophosphate synthetase; Provisional.
          Length = 345

 Score = 27.4 bits (61), Expect = 2.1
 Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 47  LSSIMEVRRNLISSDQEKMDSA-KREVESMISSYEESLAIARAHAKEIIDKVVAA 100
           LS + E   +LI   +E+ +    + +E M +S   +L   R   +E+ +K+  A
Sbjct: 185 LSRVPEEFEDLIDITKEEKEYIINKAIELMTTSNRYALLALREAEEEVGEKIANA 239


>gnl|CDD|162545 TIGR01818, ntrC, nitrogen regulation protein NR(I).  This model
           represents NtrC, a DNA-binding response regulator that
           is phosphorylated by NtrB and interacts with sigma-54.
           NtrC usually controls the expression of glutamine
           synthase, GlnA, and may be called GlnL, GlnG, etc.
          Length = 463

 Score = 27.4 bits (61), Expect = 2.3
 Identities = 12/27 (44%), Positives = 18/27 (66%), Gaps = 2/27 (7%)

Query: 96  KVVAAAEQNLE--FQREVFEKDLLHKL 120
           ++VAA  QNLE   ++  F +DL H+L
Sbjct: 271 RIVAATHQNLEALVRQGKFREDLFHRL 297


>gnl|CDD|169751 PRK09260, PRK09260, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
          Length = 288

 Score = 27.1 bits (60), Expect = 2.6
 Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 24/78 (30%)

Query: 57  LISSDQEKMDSAKREVESMIS--------------------SYEESLAIARAHAKEIIDK 96
           L+   QE+++SA++E+ S+                      SY   L  A A A    D 
Sbjct: 29  LVDIKQEQLESAQQEIASIFEQGVARGKLTEAARQAALARLSYSLDLKAAVADA----DL 84

Query: 97  VVAAAEQNLEFQREVFEK 114
           V+ A  + LE ++ VFE 
Sbjct: 85  VIEAVPEKLELKKAVFET 102


>gnl|CDD|184060 PRK13453, PRK13453, F0F1 ATP synthase subunit B; Provisional.
          Length = 173

 Score = 26.8 bits (59), Expect = 3.2
 Identities = 28/141 (19%), Positives = 66/141 (46%), Gaps = 3/141 (2%)

Query: 30  IIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEESLAIARAH 89
           + F +   +  +F    L  +M+ R   I+ D +  + AK   + +    ++ L   +  
Sbjct: 26  LTFIVLLALLKKFAWGPLKDVMDKRERDINRDIDDAEQAKLNAQKLEEENKQKLKETQEE 85

Query: 90  AKEII-DKVVAAAEQNLEFQREVFEKDLLHKLSNAQNEIDDMQKKASQEVYSIVGEVTKD 148
            ++I+ D  V A +Q  +   E   +     +  AQ+EI+  +++A  ++ + V E++  
Sbjct: 86  VQKILEDAKVQARQQQEQIIHEANVR-ANGMIETAQSEINSQKERAIADINNQVSELSVL 144

Query: 149 LVRK-LGFSVSDADVQKILDR 168
           +  K L   +S+ D + ++D+
Sbjct: 145 IASKVLRKEISEQDQKALVDK 165


>gnl|CDD|117334 pfam08764, Coagulase, Staphylococcus aureus coagulase.
           Staphylococcus aureus secretes a cofactor called
           coagulase. Coagulase is an extracellular protein that
           forms a complex with human prothrombin, and activates it
           without the usual proteolytic cleavages. The resulting
           complex directly initiates blood clotting.
          Length = 282

 Score = 26.7 bits (59), Expect = 3.3
 Identities = 14/40 (35%), Positives = 27/40 (67%), Gaps = 2/40 (5%)

Query: 106 EFQREVFEKDLLHKLSNAQNEIDDMQKKASQEVYSIVGEV 145
           +F++EV  K++  K S+ +   ++ +KKA+ EVY +V E+
Sbjct: 129 DFKKEV--KEIQSKNSDLKPYSEEEEKKATDEVYDLVSEI 166


>gnl|CDD|129194 TIGR00086, smpB, SsrA-binding protein.  This model describes the
           SsrA-binding protein, also called tmRNA binding protein,
           small protein B, and SmpB. The small, stable RNA SsrA
           (also called tmRNA or 10Sa RNA) recognizes stalled
           ribosomes such as occur during translation from message
           that lacks a stop codon. It becomes charged with Ala
           like a tRNA, then acts as mRNA to resume translation
           started with the defective mRNA. The short C-terminal
           peptide tag added by the SsrA system marks the
           abortively translated protein for degradation. SmpB
           binds SsrA after its aminoacylation but before the
           coupling of the Ala to the nascent polypeptide chain and
           is an essential part of the SsrA peptide tagging system.
           SmpB has been associated with the survival of bacterial
           pathogens in conditions of stress. It is universal in
           the first 100 sequenced bacterial genomes.
          Length = 144

 Score = 26.8 bits (60), Expect = 3.5
 Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 5/29 (17%)

Query: 114 KDLLHKLSNAQNEIDDMQKKASQEVYSIV 142
           K LLHK      EID +Q K  ++  ++V
Sbjct: 76  KLLLHK-----KEIDKLQGKVKEKGLTLV 99


>gnl|CDD|180481 PRK06231, PRK06231, F0F1 ATP synthase subunit B; Validated.
          Length = 205

 Score = 26.7 bits (59), Expect = 3.7
 Identities = 36/174 (20%), Positives = 77/174 (44%), Gaps = 28/174 (16%)

Query: 5   SSSDFSSRFPPFDTSTFLSQFFWLAIIFGIFYWV----THRFILPRLSSIMEVRRNLISS 60
           S S  +  FP F    F++     +I+  +  ++    T RF        +  R+ LI +
Sbjct: 37  SKSIINELFPNF--WVFIAHLIAFSILLLLGIFLFWKPTQRF--------LNKRKELIEA 86

Query: 61  DQEKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKL 120
           +  + +  K++ + ++ + ++    A A AKEIID+   A  + L+  +   EK+     
Sbjct: 87  EINQANELKQQAQQLLENAKQRHENALAQAKEIIDQ---ANYEALQL-KSELEKE----- 137

Query: 121 SNAQNEIDDMQKKASQEVY---SIVGEVTKDLVRKLGFSVSDADVQKILDRKRD 171
             A  + + +  +A QE+      + E  +    +L    ++  ++K +DR+ D
Sbjct: 138 --ANRQANLIIFQARQEIEKERRELKEQLQKESVELAMLAAEELIKKKVDREDD 189


>gnl|CDD|148047 pfam06207, DUF1002, Protein of unknown function (DUF1002).  This
           protein family has no known function. Its members are
           about 300 amino acids in length. It has so far been
           detected in Firmicute bacteria and some archaebacteria.
          Length = 222

 Score = 26.4 bits (59), Expect = 4.0
 Identities = 8/24 (33%), Positives = 13/24 (54%)

Query: 125 NEIDDMQKKASQEVYSIVGEVTKD 148
            +ID+ QK+A+ E      E+  D
Sbjct: 122 EKIDEEQKEAANEELVTTSELNGD 145


>gnl|CDD|172948 PRK14473, PRK14473, F0F1 ATP synthase subunit B; Provisional.
          Length = 164

 Score = 26.4 bits (58), Expect = 4.3
 Identities = 21/82 (25%), Positives = 42/82 (51%), Gaps = 6/82 (7%)

Query: 52  EVRRNLISSDQE---KMDSAKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQNLEFQ 108
           +VR  L ++ ++   ++  A++E   +++  +E    ARA   EII +    AE+  E  
Sbjct: 53  KVREQLANAKRDYEAELAKARQEAAKIVAQAQER---ARAQEAEIIAQARREAEKIKEEA 109

Query: 109 REVFEKDLLHKLSNAQNEIDDM 130
           R   E++    LS  +++I D+
Sbjct: 110 RAQAEQERQRMLSELKSQIADL 131


>gnl|CDD|184019 PRK13387, PRK13387, 1,4-dihydroxy-2-naphthoate
           octaprenyltransferase; Provisional.
          Length = 317

 Score = 26.3 bits (58), Expect = 4.3
 Identities = 10/49 (20%), Positives = 18/49 (36%), Gaps = 6/49 (12%)

Query: 21  FLSQFFWLAIIF--GIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDS 67
           F + +  +A+I   G          L    ++ +   NL S  +E  D 
Sbjct: 242 FYASYLAIAVIVLMGYISPWA----LLSFLTLRKPISNLQSFQKEAKDP 286


>gnl|CDD|178760 PLN03221, PLN03221, rapid alkalinization factor 23; Provisional.
          Length = 137

 Score = 26.2 bits (57), Expect = 4.9
 Identities = 9/16 (56%), Positives = 12/16 (75%)

Query: 3  SSSSSDFSSRFPPFDT 18
          SS S +F+  FPPF+T
Sbjct: 30 SSQSIEFAGDFPPFET 45


>gnl|CDD|131972 TIGR02926, AhaH, ATP synthase archaeal, H subunit.  he A1/A0 ATP
           synthase is homologous to the V-type (V1/V0, vacuolar)
           ATPase, but functions in the ATP synthetic direction as
           does the F1/F0 ATPase of bacteria. The hydrophilic A1
           "stalk" complex (AhaABCDEFG) is the site of ATP
           generation and is coupled to the membrane-embedded
           proton translocating A0 complex. It is unclear precisely
           where AhaH fits into these complexes.
          Length = 85

 Score = 26.0 bits (57), Expect = 5.2
 Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 4/72 (5%)

Query: 67  SAKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQ----NLEFQREVFEKDLLHKLSN 122
            A+  +E      ++ +A AR  A+E++++    A +     ++   E  EK+       
Sbjct: 10  DAEELIEEAEEERKQRIAEAREEARELLEEAEEEASKLGEEIIKEAEEEIEKEAEKIREE 69

Query: 123 AQNEIDDMQKKA 134
            + EI+ M+ KA
Sbjct: 70  GEKEIEAMKSKA 81


>gnl|CDD|181438 PRK08471, flgK, flagellar hook-associated protein FlgK; Validated.
          Length = 613

 Score = 26.2 bits (58), Expect = 5.3
 Identities = 12/46 (26%), Positives = 24/46 (52%), Gaps = 4/46 (8%)

Query: 100 AAEQNLEFQREVFEKDLLHKLSNAQNEIDDMQKKASQEVYSIVGEV 145
           A +Q L  + E     L + + + +  +D +QKK ++E+   V E+
Sbjct: 132 AQKQALAQKTET----LTNNIKDTRERLDTLQKKVNEELKVTVDEI 173


>gnl|CDD|163430 TIGR03718, R_switched_Alx, integral membrane protein, TerC family. 
           Rfam model RF00080 describes a structured RNA element
           called the yybP-ykoY leader, or SraF, which may precede
           one or several genes in a genome. Members of this highly
           hydrophobic protein family often are preceded by a
           yybP-ykoY leader, which may serve as a riboswitch. From
           the larger group of TerC homologs (pfam03741), this
           subfamily contains TerC itself from Alcaligenes sp.
           plasmid IncHI2 pMER610 and from Proteus mirabilis. It
           also contains the alkaline-inducible E. coli protein
           Alx, which unlike the two TerC examples is preceded by a
           yybP-ykoY leader.
          Length = 302

 Score = 26.0 bits (58), Expect = 5.4
 Identities = 8/21 (38%), Positives = 11/21 (52%)

Query: 19  STFLSQFFWLAIIFGIFYWVT 39
           +  + QF W+  IFG F   T
Sbjct: 120 AALIEQFHWVLYIFGAFLLYT 140


>gnl|CDD|162740 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
           primarily archaeal type.  SMC (structural maintenance of
           chromosomes) proteins bind DNA and act in organizing and
           segregating chromosomes for partition. SMC proteins are
           found in bacteria, archaea, and eukaryotes. It is found
           in a single copy and is homodimeric in prokaryotes, but
           six paralogs (excluded from this family) are found in
           eukarotes, where SMC proteins are heterodimeric. This
           family represents the SMC protein of archaea and a few
           bacteria (Aquifex, Synechocystis, etc); the SMC of other
           bacteria is described by TIGR02168. The N- and
           C-terminal domains of this protein are well conserved,
           but the central hinge region is skewed in composition
           and highly divergent.
          Length = 1164

 Score = 26.2 bits (58), Expect = 5.4
 Identities = 19/98 (19%), Positives = 45/98 (45%), Gaps = 3/98 (3%)

Query: 39  THRFILPRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEESLAIARAHAKEIIDKVV 98
               I  RL  I E + N ++ ++E ++   +E++      +E +  +     E ++   
Sbjct: 806 EVSRIEARLREI-EQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIK-SIEKEIENLNGKK 863

Query: 99  AAAEQNLEFQREVFEKDLLHKLSNAQNEIDDMQKKASQ 136
              E+ LE + E   +DL  +L + + E D+++ +  +
Sbjct: 864 EELEEELE-ELEAALRDLESRLGDLKKERDELEAQLRE 900


>gnl|CDD|181293 PRK08210, PRK08210, aspartate kinase I; Reviewed.
          Length = 403

 Score = 26.0 bits (58), Expect = 5.9
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 8/86 (9%)

Query: 76  ISSYEESLAIARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLSNAQNEIDDMQKKAS 135
               EE L    AH   +    V A E   + Q+EVF+      L+ A   +D +    +
Sbjct: 254 GIDVEERLITGIAHVSNVTQIKVKAKENAYDLQQEVFK-----ALAEAGISVDFINIFPT 308

Query: 136 QEVYSIVGEVT---KDLVRKLGFSVS 158
           + V+++  E +   K+++  LG   S
Sbjct: 309 EVVFTVSDEDSEKAKEILENLGLKPS 334


>gnl|CDD|148774 pfam07355, GRDB, Glycine/sarcosine/betaine reductase
          selenoprotein B (GRDB).  This family represents a
          conserved region approximately 350 residues long within
          the selenoprotein B component of the bacterial glycine,
          sarcosine and betaine reductase complexes.
          Length = 349

 Score = 25.8 bits (57), Expect = 6.0
 Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 3/39 (7%)

Query: 51 MEVRRNLISSDQ---EKMDSAKREVESMISSYEESLAIA 86
           EV   +I  D    E ++ A  E+  M+   +  L IA
Sbjct: 48 AEVVHTVICGDSYFNENIEEAVAEILEMLKEEKPDLFIA 86


>gnl|CDD|161672 TIGR00033, aroC, chorismate synthase.  Homotetramer (noted in
           E.coli) suggests reason for good conservation.
          Length = 351

 Score = 25.8 bits (57), Expect = 6.2
 Identities = 8/19 (42%), Positives = 13/19 (68%)

Query: 154 GFSVSDADVQKILDRKRDG 172
           G  +++ D+Q  LDR+R G
Sbjct: 24  GLPLTEEDIQPDLDRRRPG 42


>gnl|CDD|140176 PTZ00147, PTZ00147, plasmepsin-1; Provisional.
          Length = 453

 Score = 25.6 bits (56), Expect = 6.6
 Identities = 11/68 (16%), Positives = 24/68 (35%), Gaps = 19/68 (27%)

Query: 8  DFSSRF----PPFDTSTF---------------LSQFFWLAIIFGIFYWVTHRFILPRLS 48
          DF++ F      F+T                  L    ++ +  G+FY++    +  +  
Sbjct: 9  DFTNTFMKNESSFNTFRVDNKVKRWKIQKLFQILYVTVFIVLAGGLFYYIFENVVFQKNR 68

Query: 49 SIMEVRRN 56
           I E+ + 
Sbjct: 69 KINEIIKT 76


>gnl|CDD|147857 pfam05933, Fun_ATP-synt_8, Fungal ATP synthase protein 8 (A6L).
          This family consists of fungus specific ATP synthase
          protein 8 (EC:3.6.3.14). The family may be related to
          the ATP synthase protein 8 found in other eukaryotes
          pfam00895.
          Length = 47

 Score = 25.7 bits (57), Expect = 7.2
 Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 21 FLSQFFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISS 60
          F++Q  +   I  I  ++  ++ILPR+  +  V R  IS 
Sbjct: 9  FINQIVFTFAIISILLYLFSKYILPRIVRLY-VSRLFISK 47


>gnl|CDD|150409 pfam09730, BicD, Microtubule-associated protein Bicaudal-D.  BicD
           proteins consist of three coiled-coiled domains and are
           involved in dynein-mediated minus end-directed transport
           from the Golgi apparatus to the endoplasmic reticulum
           (ER). For full functioning they bind with GSK-3beta
           pfam05350 to maintain the anchoring of microtubules to
           the centromere. It appears that amino-acid residues
           437-617 of BicD and the kinase activity of GSK-3 are
           necessary for the formation of a complex between BicD
           and GSK-3beta in intact cells.
          Length = 711

 Score = 25.6 bits (56), Expect = 7.5
 Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 2/33 (6%)

Query: 105 LEFQREVFEKDLLHKLSNAQNEIDDMQKKASQE 137
           LE Q E+  K L  +LSN Q E + +   + + 
Sbjct: 37  LELQAEL--KQLRAELSNVQAENERLSSLSQEL 67


>gnl|CDD|180516 PRK06292, PRK06292, dihydrolipoamide dehydrogenase; Validated.
          Length = 460

 Score = 25.5 bits (57), Expect = 7.6
 Identities = 6/27 (22%), Positives = 11/27 (40%), Gaps = 2/27 (7%)

Query: 152 KLGFSVSDADV--QKILDRKRDGIDAF 176
           + G       +  +K++ R R   D F
Sbjct: 67  EFGIHADGPKIDFKKVMARVRRERDRF 93


>gnl|CDD|184661 PRK14405, PRK14405, membrane protein; Provisional.
          Length = 202

 Score = 25.5 bits (56), Expect = 8.2
 Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 10/45 (22%)

Query: 25  FFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAK 69
           + WL++I  IF +  HR      ++I      L+S  + K+   K
Sbjct: 165 YIWLSLIIAIFAFWRHR------TNI----VRLLSGTENKLGKKK 199


>gnl|CDD|118258 pfam09726, Macoilin, Transmembrane protein.  This entry is a highly
           conserved protein present in eukaryotes.
          Length = 680

 Score = 25.3 bits (55), Expect = 9.3
 Identities = 24/91 (26%), Positives = 39/91 (42%), Gaps = 9/91 (9%)

Query: 46  RLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQNL 105
           RL S  + R N      E+    K E E+       + A A A  +E  +  +  A+Q+L
Sbjct: 484 RLKSEADSRVNAEKQLAEEKKRKKEEEETA----ARAAAQAAASREECAE-SLKQAKQDL 538

Query: 106 EFQREVFEKDLLHKLSNAQNEIDDMQKKASQ 136
           E +     K L H L   + E   ++K+A +
Sbjct: 539 EMEI----KKLEHDLKLKEEECRMLEKEAQE 565


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.319    0.132    0.359 

Gapped
Lambda     K      H
   0.267   0.0640    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,761,169
Number of extensions: 166459
Number of successful extensions: 784
Number of sequences better than 10.0: 1
Number of HSP's gapped: 768
Number of HSP's successfully gapped: 123
Length of query: 176
Length of database: 5,994,473
Length adjustment: 87
Effective length of query: 89
Effective length of database: 4,114,577
Effective search space: 366197353
Effective search space used: 366197353
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: 54 (24.8 bits)