RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 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|31055 COG0711, AtpF, F0F1-type ATP synthase, subunit b [Energy production
and conversion].
Length = 161
Score = 69.9 bits (171), Expect = 3e-13
Identities = 39/145 (26%), Positives = 74/145 (51%), Gaps = 1/145 (0%)
Query: 25 FFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEESLA 84
W I F I W+ +F+ + ++ R+ I+ D + + K E +++++ YE+ L
Sbjct: 9 ILWQLIAFVILLWLLKKFVWKPILKALDERQAKIADDLAEAERLKEEAQALLAEYEQELE 68
Query: 85 IARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLSNAQNEIDDMQKKASQEVYSIVGE 144
AR A EII++ AEQ E + E++L A+ EI+ +++A +E+ + V E
Sbjct: 69 EAREQASEIIEQAKKEAEQIAEEIKAEAEEELERIKEAAEAEIEAEKERALEELRAEVAE 128
Query: 145 VTKDLVRK-LGFSVSDADVQKILDR 168
+ + K LG V +A + ++D
Sbjct: 129 LAVAIAEKLLGKKVDEAAQKDLIDA 153
>gnl|CDD|109486 pfam00430, ATP-synt_B, ATP synthase B/B' CF(0). Part of the CF(0)
(base unit) of the ATP synthase. The base unit is
thought to translocate protons through membrane (inner
membrane in mitochondria, thylakoid membrane in plants,
cytoplasmic membrane in bacteria). The B subunits are
thought to interact with the stalk of the CF(1)
subunits. This domain should not be confused with the ab
CF(1) proteins (in the head of the ATP synthase) which
are found in pfam00006.
Length = 132
Score = 55.0 bits (133), Expect = 1e-08
Identities = 31/129 (24%), Positives = 61/129 (47%)
Query: 25 FFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEESLA 84
I F I + F L I++ R+ I+++ ++ + ++ ++++ E+ LA
Sbjct: 2 LETNLINFLILVGLLIYFGYKPLGKILDERKEKIANNIKEAEERLKQAAALLAEAEQQLA 61
Query: 85 IARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLSNAQNEIDDMQKKASQEVYSIVGE 144
ARA A EII+ A++ E +KD L +A+ EI+ +++A E+ V
Sbjct: 62 QARAEASEIINNAKKEAQKLKEEILAEAQKDAERLLESARAEIEQEKEQALAELRQQVAA 121
Query: 145 VTKDLVRKL 153
+ + KL
Sbjct: 122 LAVQIAEKL 130
>gnl|CDD|111240 pfam02326, YMF19, Plant ATP synthase F0. This family corresponds
to subunit 8 (YMF19) of the F0 complex of plant and
algae mitochondrial F-ATPases (EC:3.6.1.34).
Length = 84
Score = 51.6 bits (124), Expect = 1e-07
Identities = 21/59 (35%), Positives = 34/59 (57%)
Query: 14 PPFDTSTFLSQFFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREV 72
P D T+ +QFFWL + F FY FILP++S I+++R+ L+SS ++ +
Sbjct: 1 PQLDKFTYFTQFFWLCLFFFTFYIFLLNFILPKISRILKLRKKLLSSLISSKLGKEQSL 59
>gnl|CDD|177224 MTH00169, ATP8, ATP synthase F0 subunit 8; Provisional.
Length = 67
Score = 40.4 bits (95), Expect = 3e-04
Identities = 18/60 (30%), Positives = 36/60 (60%), Gaps = 2/60 (3%)
Query: 14 PPFDTSTFLSQFFW-LAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREV 72
P D+ T+L+Q+ W L I+F +F + + +ILP++ + +R ++S + K + K E+
Sbjct: 2 PQLDSVTYLTQYIWTLIILFFLFSLLVN-YILPKIQQQLVIRTKGVNSVEGKKERPKIEI 60
>gnl|CDD|146524 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 33.8 bits (78), Expect = 0.027
Identities = 15/113 (13%), Positives = 46/113 (40%), Gaps = 11/113 (9%)
Query: 45 PRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQN 104
P + + Q ++ ++E++ ++ A A++ + + +Q
Sbjct: 31 PAGKAAQKQLEKEFKKLQAELQKKQKELQKEEQKLQKQAATLSEEARKAKQQELQQKQQE 90
Query: 105 LEFQREVFEKDLLHKLSNAQNEIDDMQKKASQEVYSIVGEVTKDLVRKLGFSV 157
L+ +++ AQ E+ Q++ Q +Y + + K++ ++ G+ +
Sbjct: 91 LQQKQQ-----------AAQQELQQKQQELLQPIYDKIDKAIKEVAKEKGYDL 132
>gnl|CDD|113511 pfam04744, Monooxygenase_B, Monooxygenase subunit B protein.
Family of membrane associated monooxygenases (EC
1.13.12.-) which utilize O(2) to oxidize their
substrate. Family members include both ammonia and
methane monooxygenases involved in the oxidation of
their respective substrates. These enzymes are
multi-subunit complexes. This family represents the B
subunit of the enzyme; the A subunit is thought to
contain the active site..
Length = 381
Score = 33.6 bits (77), Expect = 0.029
Identities = 10/41 (24%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 25 FFWLAI-IFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEK 64
FW+ + I I YW LPR ++ + + +K
Sbjct: 160 LFWMILGIAWIGYWFRRPMFLPRYLRVLAGGDDELVDAMDK 200
>gnl|CDD|109739 pfam00695, vMSA, Major surface antigen from hepadnavirus.
Length = 364
Score = 31.1 bits (70), Expect = 0.19
Identities = 13/50 (26%), Positives = 19/50 (38%), Gaps = 1/50 (2%)
Query: 2 ASSSSSDFSSRFPPFDTSTFLSQFFWLAIIFGIFYWVTHRF-ILPRLSSI 50
AS+ S S P S +S WL +I+ + W IL +
Sbjct: 309 ASARFSWLSLLVPSVQWSVGVSLTVWLLLIWMTWSWGPQLLSILTPFIPL 358
>gnl|CDD|37742 KOG2531, KOG2531, KOG2531, Sugar (pentulose and hexulose) kinases
[Carbohydrate transport and metabolism].
Length = 545
Score = 29.9 bits (67), Expect = 0.43
Identities = 27/120 (22%), Positives = 52/120 (43%), Gaps = 22/120 (18%)
Query: 40 HRFILPRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVA 99
RF P++ I + E + +R S++SS+ SL + + D
Sbjct: 170 ERFTGPQIRKIYQQE-------PEAYEKTERI--SLVSSFLASLLLGSYAPIDESD---- 216
Query: 100 AAEQNL-EFQREVFEKDLLHKLSNAQNEIDDMQKKASQEV--YSIVGEVTKDLVRKLGFS 156
+ NL + +++ + K LL + D+++K + V SI G ++K V++ GF
Sbjct: 217 GSGMNLLDIRKKKWSKALLDACAP------DLEEKLGKPVPPMSIAGTISKYFVKRYGFP 270
>gnl|CDD|37135 KOG1924, KOG1924, KOG1924, RhoA GTPase effector DIA/Diaphanous
[Signal transduction mechanisms, Cytoskeleton].
Length = 1102
Score = 29.2 bits (65), Expect = 0.59
Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 12/71 (16%)
Query: 85 IARAHAKEIIDKVVAAAEQNLEFQREVFEK-------DLLHKLSNAQNEIDDMQKKASQE 137
R + + + L+ Q +VF++ +L +L + + E+DD E
Sbjct: 332 FMRDGLHKYLPDLTEINNDILDVQLKVFDEHKEDDLEELSGRLEDIRAEMDDA-----NE 386
Query: 138 VYSIVGEVTKD 148
V+ ++ KD
Sbjct: 387 VFELLANTVKD 397
>gnl|CDD|177041 CHL00118, atpG, ATP synthase CF0 B' subunit; Validated.
Length = 156
Score = 29.2 bits (66), Expect = 0.60
Identities = 24/125 (19%), Positives = 48/125 (38%), Gaps = 22/125 (17%)
Query: 28 LAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREVESMISSYEESLAIAR 87
+A+ F + + + + L +++ R+ I + K + + YE+ L+ AR
Sbjct: 28 MALQFLLLMVLLNIILYKPLLKVLDERKEYIRKNLTKASEILAKANELTKQYEQELSKAR 87
Query: 88 AHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLSNAQNEIDDMQKKASQEVYSIVGEVTK 147
A+ I + A++ +E NE+ QK S++ E TK
Sbjct: 88 KEAQLEITQSQKEAKEIVE------------------NELKQAQKYID----SLLNEATK 125
Query: 148 DLVRK 152
L +
Sbjct: 126 QLEAQ 130
>gnl|CDD|177105 MTH00025, ATP8, ATP synthase F0 subunit 8; Validated.
Length = 70
Score = 28.9 bits (65), Expect = 0.84
Identities = 13/48 (27%), Positives = 26/48 (54%)
Query: 14 PPFDTSTFLSQFFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSD 61
P DT+T+L+Q+ W I+ + + F+LP + +R++L+
Sbjct: 2 PQLDTTTYLTQYRWTLIVLFLLLFFLVFFVLPTIKRNWLIRKSLMKKG 49
>gnl|CDD|32640 COG2811, NtpF, Archaeal/vacuolar-type H+-ATPase subunit H [Energy
production and conversion].
Length = 108
Score = 28.0 bits (62), Expect = 1.4
Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 4/91 (4%)
Query: 51 MEVRRNLISSDQEKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQ----NLE 106
M ++ ++ SA E+E E+ + AR A+EII++ AE+ LE
Sbjct: 2 MMDDSEVLREIKKAEISADEEIEEAKEEAEQIIKEAREEAREIIEEAEEEAEKLAQEILE 61
Query: 107 FQREVFEKDLLHKLSNAQNEIDDMQKKASQE 137
RE E++ L+ A+ E + KA++
Sbjct: 62 EAREEAEEEAEEILAEAEKEASAILSKAAEG 92
>gnl|CDD|31739 COG1550, COG1550, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 95
Score = 27.9 bits (62), Expect = 1.6
Identities = 18/91 (19%), Positives = 37/91 (40%), Gaps = 8/91 (8%)
Query: 37 WVTHRFILPRLSSIMEVR---RNLISSDQEKMDSAKREVESMISSYEESLAIA-----RA 88
+ L + S+ E R R +++ + K + + E + IA RA
Sbjct: 5 VLECELRLYDVRSLKEKRAVLRPIVTRLKNKFNVSVAETGYQDLWQRAEIGIATVSSDRA 64
Query: 89 HAKEIIDKVVAAAEQNLEFQREVFEKDLLHK 119
A+ ++D+ + + EF+R ++ LH
Sbjct: 65 VAERVLDRALDFIDAEPEFERAETVREWLHL 95
>gnl|CDD|109186 pfam00119, ATP-synt_A, ATP synthase A chain.
Length = 217
Score = 27.6 bits (62), Expect = 1.7
Identities = 9/39 (23%), Positives = 14/39 (35%), Gaps = 1/39 (2%)
Query: 15 PFDTSTFLSQFFWLAIIFGIFYWVTHRFILP-RLSSIME 52
F + L I+F + T +P R S +E
Sbjct: 2 NFHLLSLFMLLLLLLILFLVSLATTKNLTVPSRFQSFLE 40
>gnl|CDD|153280 cd07596, BAR_SNX, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexins. 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. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 218
Score = 26.9 bits (60), Expect = 2.8
Identities = 17/93 (18%), Positives = 33/93 (35%), Gaps = 12/93 (12%)
Query: 71 EVESMISSYEESLAIARAHAKEIIDKVVAAAEQNLEFQREV-----FE-------KDLLH 118
E + I EE L A+ ++ + EF + + E + L
Sbjct: 8 EAKDYILKLEEQLKKLSKQAQRLVKRRRELGSALGEFGKALIKLAKCEEEVGGELGEALS 67
Query: 119 KLSNAQNEIDDMQKKASQEVYSIVGEVTKDLVR 151
KL A E+ + + + + + E K+ +R
Sbjct: 68 KLGKAAEELSSLSEAQANQELVKLLEPLKEYLR 100
>gnl|CDD|133462 cd06852, GT_MraY, Phospho-N-acetylmuramoyl-pentapeptide-transferase
(mraY) is an enzyme responsible for the formation of the
first lipid intermediate in the synthesis of bacterial
cell wall peptidoglycan. It catalyzes the formation of
undecaprenyl-pyrophosphoryl-N-acetylmuramoyl-
pentapeptide from UDP-MurNAc-pentapeptide and
undecaprenyl-phosphate. It is an integral membrane
protein with possibly ten transmembrane domains.
Length = 280
Score = 27.1 bits (61), Expect = 3.1
Identities = 8/30 (26%), Positives = 8/30 (26%)
Query: 9 FSSRFPPFDTSTFLSQFFWLAIIFGIFYWV 38
F T L F I GI Y
Sbjct: 87 LLYYFNGSGTLITLPFFKNGLIDLGILYIP 116
>gnl|CDD|34396 COG4785, NlpI, Lipoprotein NlpI, contains TPR repeats [General
function prediction only].
Length = 297
Score = 26.9 bits (59), Expect = 3.4
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 23 SQFFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQE 63
+ F LA+ ++ +V HR+ L LS + + + +L SDQ+
Sbjct: 257 TALFKLAVANNVYNFVEHRYALLELSLLGQDQDDLAESDQQ 297
>gnl|CDD|38173 KOG2962, KOG2962, KOG2962, Prohibitin-related membrane protease
subunits [General function prediction only].
Length = 322
Score = 26.6 bits (58), Expect = 3.5
Identities = 22/103 (21%), Positives = 48/103 (46%), Gaps = 16/103 (15%)
Query: 53 VRRNLISSDQEKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQN-----LEF 107
+RRN E M++ K ++ +I++ ++ + A + K V AE+N +
Sbjct: 179 IRRNF-----ELMEAEKTKL--LIAAEKQKVVEKEAETERK--KAVIEAEKNAQVAKILM 229
Query: 108 QREVFEKDLLHKLSNAQNE--IDDMQKKASQEVYSIVGEVTKD 148
Q+++ EK+ ++S ++ + + KA E Y + E +
Sbjct: 230 QQKLMEKETEKRISEIEDAAFLAREKSKADAEYYRALKEAEAN 272
>gnl|CDD|110172 pfam01150, GDA1_CD39, GDA1/CD39 (nucleoside phosphatase) family.
Length = 424
Score = 26.6 bits (59), Expect = 3.6
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 19 STFLSQFFWLAIIF----GIFYWVTHRFILPRLSSIMEVRRN 56
STF + II G++ W+T ++L R E R
Sbjct: 118 STFPVDDQGVRIIDGAEEGLYGWITVNYLLGRFGKDPEQCRQ 159
>gnl|CDD|31648 COG1459, PulF, Type II secretory pathway, component PulF [Cell
motility and secretion / Intracellular trafficking and
secretion].
Length = 397
Score = 26.7 bits (59), Expect = 3.9
Identities = 26/144 (18%), Positives = 57/144 (39%), Gaps = 22/144 (15%)
Query: 16 FDTSTFLSQFFWL-----AIIFGIFYWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAK- 69
S FL ++ WL II + + + R + +R L K A+
Sbjct: 207 LALSDFLREWGWLLLLIIIIIAIGYLLLLRKPAGRRRLDRLLLRLPLFGKLVRKYALARF 266
Query: 70 -REVESMISS---YEESLAIA-----RAHAKEIIDKVVAAAEQNLEF-----QREVFEKD 115
R + +++SS E+L IA A ++ +++++ + + +F
Sbjct: 267 ARTLGTLLSSGVPLLEALDIAAETVSNAFLRQALEEIIQEVREGGSLSQALEKTGLFPPL 326
Query: 116 LLHKLSNAQ--NEIDDMQKKASQE 137
LL ++ + ++D+M +K +
Sbjct: 327 LLQMIAVGEESGKLDEMLEKVADF 350
>gnl|CDD|38736 KOG3527, KOG3527, KOG3527, Erythrocyte membrane protein 4.1 and
related proteins of the ERM family [General function
prediction only].
Length = 975
Score = 26.6 bits (58), Expect = 4.2
Identities = 22/99 (22%), Positives = 37/99 (37%), Gaps = 7/99 (7%)
Query: 57 LISSDQEKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQNLEFQREVFEKDL 116
L+ S + + + E S Y A KE+ DKV E + + +
Sbjct: 149 LLGSYTVQSELGDYDPEEHGSDYLSDFKFAPNQTKELEDKV---MELHKTHRGMTPAEAE 205
Query: 117 LHKLSNAQNE----IDDMQKKASQEVYSIVGEVTKDLVR 151
+H L NA+ +D K S+ V ++G L+
Sbjct: 206 IHFLENAKKLSMYGVDLHHAKDSEGVDIMLGVCASGLLI 244
>gnl|CDD|146416 pfam03763, Remorin_C, Remorin, C-terminal region. Remorins are
plant-specific plasma membrane-associated proteins. In
tobacco remorin co-purifies with lipid rafts. Most
remorins have a variable, proline-rich C-half and a more
conserved N-half that is predicted to form coiled coils.
Consistent with this, circular dichroism studies have
demonstrated that much of the protein is alpha-helical.
Remorins exist in plasma membrane preparations as
oligomeric structures and form filaments in vitro. The
proteins can bind polyanions including the extracellular
matrix component oligogalacturonic acid (OGA). In vitro,
remorin in plasma membrane preparations is
phosphorylated (principally on threonine residues) in
the presence of OGA and thus co-purifies with a protein
kinases(s). The biological functions of remorins are
unknown but roles as components of the
membrane/cytoskeleton are possible.
Length = 112
Score = 26.5 bits (59), Expect = 4.4
Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 8/74 (10%)
Query: 69 KREVESMISSYEESL---AIARAHAKEII-----DKVVAAAEQNLEFQREVFEKDLLHKL 120
K EVE+ ++EE+ R +E +K A AE L+ EK +
Sbjct: 3 KEEVEAKADAWEEAEKAKINNRYKREEAKIQAWENKKKAKAEAELKKIERKLEKKKAEAM 62
Query: 121 SNAQNEIDDMQKKA 134
+N++ KKA
Sbjct: 63 EKLKNKLAAAHKKA 76
>gnl|CDD|38067 KOG2856, KOG2856, KOG2856, Adaptor protein PACSIN [Signal
transduction mechanisms, Intracellular trafficking,
secretion, and vesicular transport, Cytoskeleton].
Length = 472
Score = 26.2 bits (57), Expect = 4.7
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 62 QEKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVAAAE--QNLEFQREVFEKDLLHK 119
Q++++ K+EV+ YE++LA + ++ + E Q E +R F K++L K
Sbjct: 183 QDRVEKCKQEVQKTKEKYEKTLAELNKYTPVYMEDMEQVFEQCQQFEEKRLQFFKEILLK 242
Query: 120 L 120
+
Sbjct: 243 V 243
>gnl|CDD|35676 KOG0455, KOG0455, KOG0455, Homoserine dehydrogenase [Amino acid
transport and metabolism].
Length = 364
Score = 26.1 bits (57), Expect = 5.5
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 115 DLLHKLSNAQNEIDDMQKKASQE--VYSIVGEV 145
+ LH L I++ K+AS E V VG +
Sbjct: 262 EFLHGLVKLDQNIEERVKEASSEGKVLRFVGVI 294
>gnl|CDD|37313 KOG2102, KOG2102, KOG2102, Exosomal 3'-5' exoribonuclease complex,
subunit Rrp44/Dis3 [Translation, ribosomal structure and
biogenesis].
Length = 941
Score = 26.2 bits (57), Expect = 5.6
Identities = 18/112 (16%), Positives = 29/112 (25%), Gaps = 14/112 (12%)
Query: 59 SSDQEKMDSAKREVESMISSYEESLAIARAHAKEIIDKV----VAAAEQNLEFQREVFEK 114
+E M A V I + SLA+ R H + E K
Sbjct: 667 FLVEEFMLLANISVAEKILASFPSLALLRRHPSPPPENFKPLVSLCLELGFNLDTSSS-K 725
Query: 115 DLLHKLSNAQNEIDDMQ---------KKASQEVYSIVGEVTKDLVRKLGFSV 157
L L +++ + ++ VY G G +
Sbjct: 726 SLADSLDRIRDDDKPYLNTLLRILATRSMTRAVYFCSGSSDTPQFHHYGLAS 777
>gnl|CDD|35729 KOG0509, KOG0509, KOG0509, Ankyrin repeat and DHHC-type Zn-finger
domain containing proteins [General function prediction
only].
Length = 600
Score = 26.1 bits (57), Expect = 5.9
Identities = 10/44 (22%), Positives = 13/44 (29%), Gaps = 1/44 (2%)
Query: 10 SSRFPPFDTSTFLSQFFWLAIIFGIFYWVTHRFILPRLSSIMEV 53
PP + FLS FW F + I+ V
Sbjct: 336 FLLRPPLLSGFFLSTLFWF-YYFWFSKITPYTLFDFHYCFIISV 378
>gnl|CDD|133283 cd01883, EF1_alpha, Eukaryotic elongation factor 1 (EF1) alpha
subfamily. EF1 is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to the ribosomes. EF1 is
composed of four subunits: the alpha chain which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This subfamily is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea
(aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha
interacts with the actin of the eukaryotic cytoskeleton
and may thereby play a role in cellular transformation
and apoptosis. EF-Tu can have no such role in bacteria.
In humans, the isoform eEF1A2 is overexpressed in 2/3
of breast cancers and has been identified as a putative
oncogene. This subfamily also includes Hbs1, a G
protein known to be important for efficient growth and
protein synthesis under conditions of limiting
translation initiation in yeast, and to associate with
Dom34. It has been speculated that yeast Hbs1 and Dom34
proteins may function as part of a complex with a role
in gene expression.
Length = 219
Score = 25.9 bits (58), Expect = 5.9
Identities = 11/36 (30%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 125 NEIDDMQKKASQEVY-SIVGEVTKDLVRKLGFSVSD 159
N++DD+ S+E Y I E++ ++K+G++ D
Sbjct: 145 NKMDDVTVNWSEERYDEIKKELSP-FLKKVGYNPKD 179
>gnl|CDD|146007 pfam03169, OPT, OPT oligopeptide transporter protein. The OPT
family of oligopeptide transporters is distinct from the
ABC pfam00005 and PTR pfam00854 transporter families.
OPT transporters were first recognized in fungi (Candida
albicans and Schizosaccharomyces pombe), but this
alignment also includes orthologues from Arabidopsis
thaliana. OPT transporters are thought to have 12-14
transmembrane domains and contain the following motif:
SPYxEVRxxVxxxDDP.
Length = 605
Score = 26.1 bits (58), Expect = 6.1
Identities = 8/26 (30%), Positives = 12/26 (46%), Gaps = 1/26 (3%)
Query: 25 FFWLAIIFGIFYWVTHRFILPRLSSI 50
F + ++YW +I P LSS
Sbjct: 162 FLIGFVASFVYYWFP-FYIFPALSSF 186
>gnl|CDD|177205 MTH00148, ND3, NADH dehydrogenase subunit 3; Provisional.
Length = 117
Score = 25.6 bits (57), Expect = 7.4
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 12/33 (36%)
Query: 3 SSSSSDFSSRFPPFDTSTFLSQFFWLAIIFGIF 35
SS+ S FS RF F LAI+F +F
Sbjct: 47 SSARSPFSLRF------------FLLAILFLVF 67
>gnl|CDD|144473 pfam00888, Cullin, Cullin family.
Length = 605
Score = 25.7 bits (56), Expect = 8.2
Identities = 21/104 (20%), Positives = 37/104 (35%), Gaps = 4/104 (3%)
Query: 21 FLSQFFWLAIIFGIF--YWVTHRFILPRLSSIMEVRRNLISSDQEKMDSAKREVESMISS 78
F + L IF Y+V + + +++ R + D + +I
Sbjct: 80 FSTSMKILNNIFMYLNRYYVKRKEVYEIYELGLDIWRESLF--DPIKDKLIDALLRLIEK 137
Query: 79 YEESLAIARAHAKEIIDKVVAAAEQNLEFQREVFEKDLLHKLSN 122
I R+ K ++D V + +L +E FEK L S
Sbjct: 138 ERLGEIIDRSLIKNVLDMFVELGDDSLSVYKEDFEKPFLEATSE 181
>gnl|CDD|133351 cd04151, Arl1, Arl1 subfamily. Arl1 (Arf-like 1) localizes to the
Golgi complex, where it is believed to recruit effector
proteins to the trans-Golgi network. Like most members
of the Arf family, Arl1 is myristoylated at its
N-terminal helix and mutation of the myristoylation site
disrupts Golgi targeting. In humans, the
Golgi-localized proteins golgin-97 and golgin-245 have
been identified as Arl1 effectors. Golgins are large
coiled-coil proteins found in the Golgi, and these
golgins contain a C-terminal GRIP domain, which is the
site of Arl1 binding. Additional Arl1 effectors include
the GARP (Golgi-associated retrograde protein)/VFT
(Vps53) vesicle-tethering complex and Arfaptin 2. Arl1
is not required for exocytosis, but appears necessary
for trafficking from the endosomes to the Golgi. In
Drosophila zygotes, mutation of Arl1 is lethal, and in
the host-bloodstream form of Trypanosoma brucei, Arl1 is
essential for viability.
Length = 158
Score = 25.4 bits (56), Expect = 8.9
Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 13/72 (18%)
Query: 59 SSDQEKMDSAKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQNLE---FQREVFEKD 115
S+D++++ +AK E+ +M+ EE L ++ +V A +Q++ + E+ EK
Sbjct: 76 STDRDRLGTAKEELHAMLE--EEEL------KGAVL--LVFANKQDMPGALSEAEISEKL 125
Query: 116 LLHKLSNAQNEI 127
L +L + I
Sbjct: 126 GLSELKDRTWSI 137
>gnl|CDD|153290 cd07606, BAR_SFC_plant, The Bin/Amphiphysin/Rvs (BAR) domain of the
plant protein SCARFACE (SFC). 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. The plant protein SCARFACE (SFC), also called
VAscular Network 3 (VAN3), is a plant ACAP (ArfGAP with
Coiled-coil, ANK repeat and PH domain containing
protein), an Arf GTPase Activating Protein (GAP) that
plays a role in the trafficking of auxin efflux
regulators from the plasma membrane to the endosome. It
is required for the normal vein patterning in leaves.
SCF contains an N-terminal BAR domain, followed by a
Pleckstrin Homology (PH) domain, an Arf GAP domain, and
C-terminal ankyrin (ANK) repeats. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions.
Length = 202
Score = 25.5 bits (56), Expect = 9.1
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 68 AKREVESMISSYEESLAIARAHAKEIIDKVVAAAEQNLEFQREVFEK---DLLHKLSNA 123
A+R + YE++ + + K+ +++AAAE++L R FE DL+++L A
Sbjct: 108 ARRRFDKASLDYEQARSKFLSLTKDAKPEILAAAEEDLGTTRSAFETARFDLMNRLHAA 166
>gnl|CDD|110765 pfam01790, LGT, Prolipoprotein diacylglyceryl transferase.
Length = 257
Score = 25.2 bits (56), Expect = 9.2
Identities = 7/27 (25%), Positives = 11/27 (40%)
Query: 20 TFLSQFFWLAIIFGIFYWVTHRFILPR 46
T L + I+F I W+ R +
Sbjct: 174 TQLYESILEGIVFFIILWLRRRKKKLK 200
>gnl|CDD|164588 MTH00012, ND3, NADH dehydrogenase subunit 3; Validated.
Length = 117
Score = 25.2 bits (55), Expect = 9.4
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 8/43 (18%)
Query: 1 MASSSSSD------FSSRFPPFDTS--TFLSQFFWLAIIFGIF 35
+A+ S++D F F P T+ F +FF LAIIF +F
Sbjct: 25 LAARSTADREKTSPFECGFDPHKTARIPFSLRFFLLAIIFIVF 67
>gnl|CDD|112963 pfam04173, DoxD, TQO small subunit DoxD. Acidianus ambivalens doxD
is a subunit of the terminal quinol oxidase present in
the plasma membrane of Acidianus ambivalens, with
calculated molecular mass of 20.4 kDa.
Thiosulphate:quinone oxidoreductase (TQO) is one of the
early steps in elemental sulphur oxidation. A novel TQO
enzyme was purified from the thermo-acidophilic archaeon
Acidianus ambivalens and shown to consist of a large
subunit (DoxD) and a smaller subunit (DoxA). The DoxD-
and DoxA-like two subunits are fused together in a
single polypeptide in the terminal quinol oxidase from
Bacteroides thetaiotaomicron.
Length = 167
Score = 25.1 bits (55), Expect = 9.8
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 14 PPFDTSTFLSQFFWLAIIFGIFYWVTHRFILPRLSSIMEVRRNLI 58
PP FL F ++ IIFG+ + +L RLSS++ L
Sbjct: 61 PPLLV-GFLVMFTYVEIIFGLLMIIG---LLTRLSSLVAFYMALG 101
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.319 0.132 0.359
Gapped
Lambda K H
0.267 0.0573 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,991,933
Number of extensions: 98054
Number of successful extensions: 592
Number of sequences better than 10.0: 1
Number of HSP's gapped: 587
Number of HSP's successfully gapped: 86
Length of query: 176
Length of database: 6,263,737
Length adjustment: 87
Effective length of query: 89
Effective length of database: 4,383,754
Effective search space: 390154106
Effective search space used: 390154106
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 (24.9 bits)