RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6108
(131 letters)
>gnl|CDD|185504 PTZ00184, PTZ00184, calmodulin; Provisional.
Length = 149
Score = 141 bits (357), Expect = 3e-44
Identities = 72/143 (50%), Positives = 96/143 (67%), Gaps = 17/143 (11%)
Query: 4 LDEEQITEWKEAFALFDKNGSGKIVSKYVGTVMRAIGRNPTEQELEDLLKEVDPDDVGSV 63
L EEQI E+KEAF+LFDK+G G I +K +GTVMR++G+NPTE EL+D++ EVD D G++
Sbjct: 5 LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTI 64
Query: 64 DFESFLKLMANHIPNVDSTAELLEAFQVFDKD-----------------GEKLSDQEVDE 106
DF FL LMA + + DS E+ EAF+VFD+D GEKL+D+EVDE
Sbjct: 65 DFPEFLTLMARKMKDTDSEEEIKEAFKVFDRDGNGFISAAELRHVMTNLGEKLTDEEVDE 124
Query: 107 LIGLADENNTGHVRYEEFAKVMT 129
+I AD + G + YEEF K+M
Sbjct: 125 MIREADVDGDGQINYEEFVKMMM 147
>gnl|CDD|227455 COG5126, FRQ1, Ca2+-binding protein (EF-Hand superfamily) [Signal
transduction mechanisms / Cytoskeleton / Cell division
and chromosome partitioning / General function
prediction only].
Length = 160
Score = 104 bits (261), Expect = 1e-29
Identities = 56/142 (39%), Positives = 80/142 (56%), Gaps = 18/142 (12%)
Query: 4 LDEEQITEWKEAFALFDKNGSGKIVSKYVGTVMRAIGRNPTEQELEDLLKEVDPDDVGSV 63
L EEQI E KEAF LFD++ G I +G ++R++G NP+E E+ L E +V
Sbjct: 14 LTEEQIQELKEAFQLFDRDSDGLIDRNELGKILRSLGFNPSEAEINKLF-EEIDAGNETV 72
Query: 64 DFESFLKLMANHIPNVDSTAELLEAFQVFDKD-----------------GEKLSDQEVDE 106
DF FL +M+ + D EL EAF++FDKD GE+LSD+EV++
Sbjct: 73 DFPEFLTVMSVKLKRGDKEEELREAFKLFDKDHDGYISIGELRRVLKSLGERLSDEEVEK 132
Query: 107 LIGLADENNTGHVRYEEFAKVM 128
L+ DE+ G + YEEF K++
Sbjct: 133 LLKEYDEDGDGEIDYEEFKKLI 154
Score = 50.0 bits (120), Expect = 1e-08
Identities = 26/63 (41%), Positives = 40/63 (63%)
Query: 11 EWKEAFALFDKNGSGKIVSKYVGTVMRAIGRNPTEQELEDLLKEVDPDDVGSVDFESFLK 70
E +EAF LFDK+ G I + V++++G +++E+E LLKE D D G +D+E F K
Sbjct: 93 ELREAFKLFDKDHDGYISIGELRRVLKSLGERLSDEEVEKLLKEYDEDGDGEIDYEEFKK 152
Query: 71 LMA 73
L+
Sbjct: 153 LIK 155
>gnl|CDD|185503 PTZ00183, PTZ00183, centrin; Provisional.
Length = 158
Score = 95.1 bits (237), Expect = 5e-26
Identities = 52/143 (36%), Positives = 80/143 (55%), Gaps = 17/143 (11%)
Query: 4 LDEEQITEWKEAFALFDKNGSGKIVSKYVGTVMRAIGRNPTEQELEDLLKEVDPDDVGSV 63
L E+Q E +EAF LFD +GSG I K + MR++G P ++E++ ++ +VD D G +
Sbjct: 11 LTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGFEPKKEEIKQMIADVDKDGSGKI 70
Query: 64 DFESFLKLMANHIPNVDSTAELLEAFQVFDKD-----------------GEKLSDQEVDE 106
DFE FL +M + D E+L+AF++FD D GE ++D+E+ E
Sbjct: 71 DFEEFLDIMTKKLGERDPREEILKAFRLFDDDKTGKISLKNLKRVAKELGETITDEELQE 130
Query: 107 LIGLADENNTGHVRYEEFAKVMT 129
+I AD N G + EEF ++M
Sbjct: 131 MIDEADRNGDGEISEEEFYRIMK 153
Score = 46.6 bits (111), Expect = 2e-07
Identities = 21/64 (32%), Positives = 37/64 (57%)
Query: 11 EWKEAFALFDKNGSGKIVSKYVGTVMRAIGRNPTEQELEDLLKEVDPDDVGSVDFESFLK 70
E +AF LFD + +GKI K + V + +G T++EL++++ E D + G + E F +
Sbjct: 91 EILKAFRLFDDDKTGKISLKNLKRVAKELGETITDEELQEMIDEADRNGDGEISEEEFYR 150
Query: 71 LMAN 74
+M
Sbjct: 151 IMKK 154
>gnl|CDD|238008 cd00051, EFh, EF-hand, calcium binding motif; A diverse
superfamily of calcium sensors and calcium signal
modulators; most examples in this alignment model have
2 active canonical EF hands. Ca2+ binding induces a
conformational change in the EF-hand motif, leading to
the activation or inactivation of target proteins.
EF-hands tend to occur in pairs or higher copy numbers.
Length = 63
Score = 58.7 bits (143), Expect = 7e-13
Identities = 26/61 (42%), Positives = 44/61 (72%)
Query: 13 KEAFALFDKNGSGKIVSKYVGTVMRAIGRNPTEQELEDLLKEVDPDDVGSVDFESFLKLM 72
+EAF LFDK+G G I + + ++++G +E+E++++++EVD D G +DFE FL+LM
Sbjct: 3 REAFRLFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLELM 62
Query: 73 A 73
A
Sbjct: 63 A 63
Score = 39.1 bits (92), Expect = 3e-05
Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 17/63 (26%)
Query: 84 ELLEAFQVFDKDG-----------------EKLSDQEVDELIGLADENNTGHVRYEEFAK 126
EL EAF++FDKDG E LS++E+DE+I D++ G + +EEF +
Sbjct: 1 ELREAFRLFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLE 60
Query: 127 VMT 129
+M
Sbjct: 61 LMA 63
Score = 24.8 bits (55), Expect = 6.1
Identities = 8/17 (47%), Positives = 9/17 (52%)
Query: 11 EWKEAFALFDKNGSGKI 27
E E DK+G GKI
Sbjct: 37 EIDEMIREVDKDGDGKI 53
>gnl|CDD|222407 pfam13833, EF_hand_6, EF-hand domain pair.
Length = 53
Score = 37.5 bits (88), Expect = 8e-05
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 36 MRAIGRNPTEQELEDLLKEVDPDDVGSVDFESFLKLMA 73
+ +G + +E+E++ L +E D D G + FE F L+
Sbjct: 14 LALLGISLSEEEVDILFREFDTDGDGKISFEEFCVLLQ 51
Score = 33.3 bits (77), Expect = 0.004
Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 20/69 (28%)
Query: 61 GSVDFESFLKLMANHIPNVDSTAELLEAFQVFDKDGEKLSDQEVDELIGLADENNTGHVR 120
G + E + +A G LS++EVD L D + G +
Sbjct: 3 GLITREELKRALA--------------------LLGISLSEEEVDILFREFDTDGDGKIS 42
Query: 121 YEEFAKVMT 129
+EEF ++
Sbjct: 43 FEEFCVLLQ 51
>gnl|CDD|215520 PLN02964, PLN02964, phosphatidylserine decarboxylase.
Length = 644
Score = 37.1 bits (86), Expect = 0.001
Identities = 33/120 (27%), Positives = 52/120 (43%), Gaps = 26/120 (21%)
Query: 14 EAFALFDKNGSGKIVSKYVGTVMRAIGRNPTEQEL---EDLLKEVDPDDVGSVDFESFLK 70
E+F L D + S K+V V +I +P E E +L VD D+ G + F F
Sbjct: 147 ESFDLLDPSSSNKVVGSI--FVSCSI-EDPVETERSFARRILAIVDYDEDGQLSFSEF-- 201
Query: 71 LMANHIPNVDSTAELLEAFQVFDKDGEKLSDQEVDELIGLADENNTGHVRYEEFAKVMTL 130
++L++AF G ++ + +EL AD N G V +E A ++ L
Sbjct: 202 ------------SDLIKAF------GNLVAANKKEELFKAADLNGDGVVTIDELAALLAL 243
Score = 28.7 bits (64), Expect = 0.85
Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 3/85 (3%)
Query: 13 KEAFALFDKNGSGKIVSKYVGTVMRAIGRNPTEQELEDLLKEVDPDDVGSVDFESFLKLM 72
+ A+ D + G++ +++A G + E+L K D + G V + L+
Sbjct: 182 RRILAIVDYDEDGQLSFSEFSDLIKAFGNLVAANKKEELFKAADLNGDGVVTIDELAALL 241
Query: 73 ANH---IPNVDSTAELLEAFQVFDK 94
A P +++ EA V DK
Sbjct: 242 ALQQEQEPIINNCPVCGEALGVSDK 266
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 32.7 bits (75), Expect = 0.006
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 17 ALFDKNGSGKI----VSKYVGTVMRAIGRNPTEQELEDLLKEVDPDDVGSVDFESFLKLM 72
L DK+G G I + K + + + E+ +E E+D D G + FE FL+ M
Sbjct: 1 KLLDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEFLEAM 60
Score = 32.0 bits (73), Expect = 0.015
Identities = 9/47 (19%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 83 AELLEAFQ-VFDKDGEKLSDQEVDELIGLADENNTGHVRYEEFAKVM 128
EL + + + K ++ ++ ++ D++ G + +EEF + M
Sbjct: 14 EELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEFLEAM 60
>gnl|CDD|197492 smart00054, EFh, EF-hand, calcium binding motif. EF-hands are
calcium-binding motifs that occur at least in pairs.
Links between disease states and genes encoding
EF-hands, particularly the S100 subclass, are emerging.
Each motif consists of a 12 residue loop flanked on
either side by a 12 residue alpha-helix. EF-hands
undergo a conformational change unpon binding calcium
ions.
Length = 29
Score = 30.8 bits (71), Expect = 0.019
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 11 EWKEAFALFDKNGSGKIVSKYVGTVMRAI 39
E KEAF LFDK+G GKI + +++A+
Sbjct: 1 ELKEAFRLFDKDGDGKIDFEEFKDLLKAL 29
Score = 27.3 bits (62), Expect = 0.32
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 103 EVDELIGLADENNTGHVRYEEFAKVMT 129
E+ E L D++ G + +EEF ++
Sbjct: 1 ELKEAFRLFDKDGDGKIDFEEFKDLLK 27
Score = 23.5 bits (52), Expect = 8.6
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 47 ELEDLLKEVDPDDVGSVDFESFLKLMAN 74
EL++ + D D G +DFE F L+
Sbjct: 1 ELKEAFRLFDKDGDGKIDFEEFKDLLKA 28
>gnl|CDD|205583 pfam13405, EF_hand_4, EF-hand domain.
Length = 30
Score = 30.3 bits (69), Expect = 0.027
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 11 EWKEAFALFDKNGSGKIVSKYVGTVMRAIG 40
E +EAF LFDK+G G I ++ + +R++G
Sbjct: 1 ELREAFKLFDKDGDGYISAEELRKALRSLG 30
>gnl|CDD|200946 pfam00036, efhand, EF hand. The EF-hands can be divided into two
classes: signaling proteins and buffering/transport
proteins. The first group is the largest and includes
the most well-known members of the family such as
calmodulin, troponin C and S100B. These proteins
typically undergo a calcium-dependent conformational
change which opens a target binding site. The latter
group is represented by calbindin D9k and do not
undergo calcium dependent conformational changes.
Length = 29
Score = 29.7 bits (68), Expect = 0.046
Identities = 12/17 (70%), Positives = 13/17 (76%)
Query: 11 EWKEAFALFDKNGSGKI 27
E KEAF FDK+G GKI
Sbjct: 1 ELKEAFKEFDKDGDGKI 17
Score = 25.9 bits (58), Expect = 1.2
Identities = 7/27 (25%), Positives = 15/27 (55%)
Query: 103 EVDELIGLADENNTGHVRYEEFAKVMT 129
E+ E D++ G + +EEF +++
Sbjct: 1 ELKEAFKEFDKDGDGKISFEEFKELLK 27
Score = 23.6 bits (52), Expect = 8.2
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 47 ELEDLLKEVDPDDVGSVDFESFLKLMAN 74
EL++ KE D D G + FE F +L+
Sbjct: 1 ELKEAFKEFDKDGDGKISFEEFKELLKK 28
>gnl|CDD|189007 cd09600, M1_APN_1, Peptidase M1 family containing Aminopeptidase N.
This family contains aminopeptidase N (APN; CD13;
Alanyl aminopeptidase; EC 3.4.11.2), a Type II integral
membrane protease belonging to the M1 gluzincin family.
It includes bacterial-type alanyl aminopeptidases as
well as PfA-M1 aminopeptidase (Plasmodium
falciparum-type). APN consists of a small N-terminal
cytoplasmic domain, a single transmembrane domain and a
large extracellular ectodomain that contains the active
site. It preferentially cleaves neutral amino acids from
the N-terminus of oligopeptides and, in higher
eukaryotes, is present in a variety of human tissues and
cell types (leukocyte, fibroblast, endothelial and
epithelial cells). APN expression is dysregulated in
inflammatory diseases such as chronic pain, rheumatoid
arthritis, multiple sclerosis, systemic sclerosis,
systemic lupus erythematosus,
polymyositis/dermatomyosytis and pulmonary sarcoidosis,
and is enhanced in tumor cells such as melanoma, renal,
prostate, pancreas, colon, gastric and thyroid cancers.
It is predominantly expressed on stem cells and on cells
of the granulocytic and monocytic lineages at distinct
stages of differentiation, thus considered a marker of
differentiation. Thus, APN inhibition may lead to the
development of anti-cancer and anti-inflammatory drugs.
APNs are also present in many pathogenic bacteria and
represent potential drug targets, Some APNs have been
used commercially, such as one from Lactococcus lactis
used in the food industry. APN also serves as a receptor
for coronaviruses, although the virus receptor
interaction site seems to be distinct from the enzymatic
site and aminopeptidase activity is not necessary for
viral infection. APNs have also been extensively studied
as putative Cry toxin receptors. Cry1 proteins are
pore-forming toxins that bind to the midgut epithelial
cell membrane of susceptible insect larvae, causing
extensive damage. Several different toxins, including
Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have
been shown to bind to APNs; however, a direct role of
APN in cytotoxicity has been yet to be firmly
established.
Length = 861
Score = 32.6 bits (75), Expect = 0.049
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 43 PTEQELEDLLKEVDPDDVGSVDFESFLKLMANHIPNVDSTAELLEAFQVFDKDGEKLSDQ 102
P+E E+ + ++ +DPD + E+ +K +A + ELLE ++ K+ E D
Sbjct: 612 PSENEIAERMEVIDPDAIHEA-REALIKQLATEL-----KDELLELYEENRKNEEYSVDA 665
Query: 103 E 103
E
Sbjct: 666 E 666
>gnl|CDD|227624 COG5308, NUP170, Nuclear pore complex subunit [Intracellular
trafficking and secretion].
Length = 1263
Score = 31.1 bits (70), Expect = 0.17
Identities = 15/58 (25%), Positives = 27/58 (46%)
Query: 46 QELEDLLKEVDPDDVGSVDFESFLKLMANHIPNVDSTAELLEAFQVFDKDGEKLSDQE 103
+EL + VGS DFESF+ ++N + + + + + D G+ D+E
Sbjct: 1115 EELMSSHENAIISPVGSSDFESFVSFLSNLLIKISKSENVFPIMDLNDIVGDIFCDKE 1172
>gnl|CDD|237669 PRK14315, glmM, phosphoglucosamine mutase; Provisional.
Length = 448
Score = 29.9 bits (68), Expect = 0.30
Identities = 19/52 (36%), Positives = 24/52 (46%), Gaps = 17/52 (32%)
Query: 92 FDKDGEKLSDQ---EVDELI------GLADENNTG--------HVRYEEFAK 126
F DG KLSD+ E++ L+ LA + G H RY EFAK
Sbjct: 114 FGPDGFKLSDEIELEIEALLDGDLDKRLAAPADIGRAKRIDDAHGRYIEFAK 165
>gnl|CDD|238009 cd00052, EH, Eps15 homology domain; found in proteins implicated
in endocytosis, vesicle transport, and signal
transduction. The alignment contains a pair of EF-hand
motifs, typically one of them is canonical and binds to
Ca2+, while the other may not bind to Ca2+. A
hydrophobic binding pocket is formed by residues from
both EF-hand motifs. The EH domain binds to proteins
containing NPF (class I), [WF]W or SWG (class II), or
H[TS]F (class III) sequence motifs.
Length = 67
Score = 28.0 bits (63), Expect = 0.48
Identities = 13/56 (23%), Positives = 18/56 (32%), Gaps = 2/56 (3%)
Query: 13 KEAFALFDKNGSGKIVSKYVGTVMRAIGRNPTEQELEDLLKEVDPDDVGSVDFESF 68
+ F D +G G I + G L + D D G +D E F
Sbjct: 2 DQIFRSLDPDGDGLISGDEARPFLGKSGL--PRSVLAQIWDLADTDKDGKLDKEEF 55
Score = 24.9 bits (55), Expect = 5.4
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 98 KLSDQEVDELIGLADENNTGHVRYEEFAKVMTL 130
L + ++ LAD + G + EEFA M L
Sbjct: 29 GLPRSVLAQIWDLADTDKDGKLDKEEFAIAMHL 61
>gnl|CDD|200466 cd11327, AmyAc_Glg_debranch_2, Alpha amylase catalytic domain found
in glycogen debranching enzymes. Debranching enzymes
facilitate the breakdown of glycogen through
glucosyltransferase and glucosidase activity. These
activities are performed by a single enzyme in mammals,
yeast, and some bacteria, but by two distinct enzymes in
Escherichia coli and other bacteria. Debranching enzymes
perform two activities, 4-alpha-D-glucanotransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33).
4-alpha-D-glucanotransferase catalyzes the
endohydrolysis of 1,6-alpha-D-glucoside linkages at
points of branching in chains of 1,4-linked
alpha-D-glucose residues. Amylo-alpha-1,6-glucosidase
catalyzes the endohydrolysis of 1,6-alpha-D-glucoside
linkages at points of branching in chains of 1,4-linked
alpha-D-glucose residues. The catalytic triad (DED),
which is highly conserved in other debranching enzymes,
is not present in this group. The Alpha-amylase family
comprises the largest family of glycoside hydrolases
(GH), with the majority of enzymes acting on starch,
glycogen, and related oligo- and polysaccharides. These
proteins catalyze the transformation of alpha-1,4 and
alpha-1,6 glucosidic linkages with retention of the
anomeric center. The protein is described as having 3
domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a
loop between the beta 3 strand and alpha 3 helix of A; C
is the C-terminal extension characterized by a Greek
key. The majority of the enzymes have an active site
cleft found between domains A and B where a triad of
catalytic residues (Asp, Glu and Asp) performs
catalysis. Other members of this family have lost the
catalytic activity as in the case of the human 4F2hc, or
only have 2 residues that serve as the catalytic
nucleophile and the acid/base, such as Thermus A4
beta-galactosidase with 2 Glu residues (GH42) and human
alpha-galactosidase with 2 Asp residues (GH31). The
family members are quite extensive and include: alpha
amylase, maltosyltransferase, cyclodextrin
glycotransferase, maltogenic amylase, neopullulanase,
isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 478
Score = 29.1 bits (66), Expect = 0.61
Identities = 33/132 (25%), Positives = 50/132 (37%), Gaps = 24/132 (18%)
Query: 3 TLDEEQITEWKEAFALFDKNGSGKIVSKYVGTVMRAIGRNPTEQELEDLLKEVDPD---D 59
LD E+ E F K+G K+ K + I + E+LL DP
Sbjct: 196 VLDVEKA---VEQFKEALKSGKPKLPKKGSDVSLADILKK------EELLIIQDPLYERF 246
Query: 60 VGSVDFESFLKLMANHIPNVDSTAELLEAFQVFDKDGEKLSD------QEVDELIGLADE 113
+VD E ++ +H + + E LE F + L + +E DE + A
Sbjct: 247 GATVDMEKAAEIFNSHRGDEERIEECLERF------RKALDELNVPLYREYDEDLNAAVN 300
Query: 114 NNTGHVRYEEFA 125
N G +RYE
Sbjct: 301 NIIGRIRYERLD 312
>gnl|CDD|227387 COG5054, ERV1, Mitochondrial sulfhydryl oxidase involved in the
biogenesis of cytosolic Fe/S proteins [Posttranslational
modification, protein turnover, chaperones].
Length = 181
Score = 28.3 bits (63), Expect = 1.00
Identities = 24/93 (25%), Positives = 34/93 (36%), Gaps = 10/93 (10%)
Query: 20 DKNGSGKIVSKYVGTVMRAIGRNPTEQELEDL------LKEVDPDDVGSVDFESFLKLMA 73
D G+ + TV PT Q+ +DL P S F+ KL+
Sbjct: 78 DVEELGRSSWTLLHTVAANYPARPTPQQRDDLRSFLFLFSITYPCGECSKHFQ---KLLD 134
Query: 74 NHIPNVDSTAELLE-AFQVFDKDGEKLSDQEVD 105
+ P V S A +V +K EKL + D
Sbjct: 135 VYPPQVSSREAATTWACEVHNKVNEKLGKPKFD 167
>gnl|CDD|218005 pfam04285, DUF444, Protein of unknown function (DUF444). Bacterial
protein of unknown function. One family member is
predicted to contain a von Willebrand factor (vWF) type
A domain (Smart:VWA).
Length = 421
Score = 27.8 bits (62), Expect = 1.6
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 6/60 (10%)
Query: 6 EEQITEWKEAFALFDKNGSGKIVSKYVGTVMRAIGRN-----PTEQELEDLLKEVDPDDV 60
+QI E+K A K+G ++K V T+ AI R P EL+ E+
Sbjct: 141 ADQIDEFKTERAGIQKSGVPANINK-VRTLRSAIKRRIALGRPKRAELDADAGELARIAR 199
>gnl|CDD|148323 pfam06648, DUF1160, Protein of unknown function (DUF1160). This
family consists of several hypothetical Baculovirus
proteins of unknown function.
Length = 122
Score = 27.2 bits (61), Expect = 1.7
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 5/62 (8%)
Query: 47 ELEDLLKEVDPDDVGSVDFESFLKLMANHIPNVDSTAELLEAFQVFDKDGEKLSDQEVDE 106
L++ LKE++ DD F + LK+ V+ +++A DG KL+ ++D
Sbjct: 21 HLKNYLKELERDDTFRDKFVTVLKMFIARKITVEDIYNIVDAV-----DGIKLTKSQIDY 75
Query: 107 LI 108
L+
Sbjct: 76 LV 77
>gnl|CDD|226003 COG3472, COG3472, Uncharacterized conserved protein [Function
unknown].
Length = 342
Score = 27.5 bits (61), Expect = 1.9
Identities = 15/85 (17%), Positives = 36/85 (42%), Gaps = 8/85 (9%)
Query: 29 SKYVGTVMRAIGRNPTEQELEDLLKEVD-PDDVGSVDFESFLK----LMANHIPNVDSTA 83
S+Y+G E+ L+++L P+ + D+++F + + + I +
Sbjct: 260 SEYLG---ELENDVNEERILDEMLIPHALPEGLWDNDYDTFFEERAENVLSEIMDAIGKY 316
Query: 84 ELLEAFQVFDKDGEKLSDQEVDELI 108
+LE+ + ++ E L +D
Sbjct: 317 SILESDERAVEETEVLVRDFIDREE 341
>gnl|CDD|192335 pfam09695, YtfJ_HI0045, Bacterial protein of unknown function
(YtfJ_HI0045). These are sequences from gamma
proteobacteria that are related to the E. coli protein,
YtfJ.
Length = 160
Score = 27.2 bits (61), Expect = 2.0
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 7/34 (20%)
Query: 88 AFQVFDKDGE-------KLSDQEVDELIGLADEN 114
A V DK G+ L+ E+ ++IGL +
Sbjct: 127 AIIVLDKQGKVLFVKEGALTPAEIQQVIGLIKKL 160
>gnl|CDD|205383 pfam13202, EF_hand_3, EF hand.
Length = 25
Score = 24.9 bits (56), Expect = 2.1
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 13 KEAFALFDKNGSGKI 27
K+ F FD NG GKI
Sbjct: 2 KDLFRQFDTNGDGKI 16
>gnl|CDD|140280 PTZ00253, PTZ00253, tryparedoxin peroxidase; Provisional.
Length = 199
Score = 27.2 bits (60), Expect = 2.3
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 70 KLMANHIP---NVDSTAELLEAFQVFDKDGE 97
++ N +P NV+ LLEAFQ +K GE
Sbjct: 141 QITVNDMPVGRNVEEVLRLLEAFQFVEKHGE 171
>gnl|CDD|147907 pfam06002, CST-I, Alpha-2,3-sialyltransferase (CST-I). This family
consists of several alpha-2,3-sialyltransferase (CST-I)
proteins largely found in Campylobacter jejuni.
Length = 291
Score = 27.0 bits (60), Expect = 2.9
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 59 DVGSVDFESFLKLMANHIPNVDSTAEL---LEAFQVFDKDGEKLSDQEV 104
++G V+ E F+K + H P+V E L+ F + K E +Q +
Sbjct: 82 NLGDVEGEQFVKQLEAHFPDVHLGYEYLKKLKEFFAYLKYHEIYYNQRI 130
>gnl|CDD|150245 pfam09506, Salt_tol_Pase, Glucosylglycerol-phosphate phosphatase
(Salt_tol_Pase). Proteins in this family are
glucosylglycerol-phosphate phosphatases, with the gene
symbol stpA (Salt Tolerance Protein A). A motif
characteristic of acid phosphatases is found, but
otherwise this family shows little sequence similarity
to other phosphatases. This enzyme acts on the
glucosylglycerol phosphate, product of glucosylglycerol
phosphate synthase and immediate precursor of the
osmoprotectant glucosylglycerol.
Length = 381
Score = 27.2 bits (61), Expect = 2.9
Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 13/63 (20%)
Query: 39 IGRNPTEQELEDLLKEVDPDDVGSVDFESFLK----------LMANHIPNVDSTAELLEA 88
+GR+ +E +K P DVG+ D + LK L+ +I N A L E
Sbjct: 200 LGRDANGRER---IKPAAPGDVGTTDIQFMLKGAIKEAGLLVLINKYIANRTGEAPLGED 256
Query: 89 FQV 91
F V
Sbjct: 257 FNV 259
>gnl|CDD|237585 PRK14015, pepN, aminopeptidase N; Provisional.
Length = 875
Score = 27.0 bits (61), Expect = 3.1
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 43 PTEQELEDLLKEVDPDDVGSVDFESFLKLMANHIPNVDSTAELLEAFQVFDKDGEKLSDQ 102
P+E EL + ++ +DPD + + E+ + +A + ELL ++ DG D
Sbjct: 623 PSEAELAEQMEVIDPDAIHAA-REALRRALATAL-----KDELLALYEALQTDGPYSPDA 676
Query: 103 E 103
E
Sbjct: 677 E 677
>gnl|CDD|221331 pfam11940, DUF3458, Domain of unknown function (DUF3458). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria, archaea and eukaryotes.
This domain is typically between 402 to 419 amino acids
in length. This domain is found associated with
pfam01433. This domain has a conserved FSAPV sequence
motif.
Length = 365
Score = 26.7 bits (60), Expect = 3.4
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 43 PTEQELEDLLKEVDPD 58
P+E EL + +K VDPD
Sbjct: 157 PSEAELAEQMKVVDPD 172
>gnl|CDD|176526 cd08584, PI-PLCc_GDPD_SF_unchar2, Uncharacterized hypothetical
proteins similar to the catalytic domains of
Phosphoinositide-specific phospholipaseand
Glycerophosphodiester phosphodiesterases. This
subfamily corresponds to a group of uncharacterized
hypothetical proteins similar to the catalytic domains
of Phosphoinositide-specific phospholipase C (PI-PLC),
and glycerophosphodiester phosphodiesterases (GP-GDE),
and also sphingomyelinases D (SMases D) and similar
proteins. They hydrolyze the 3'-5' phosphodiester bonds
in different substrates, utilizing a similar mechanism
of general base and acid catalysis involving two
conserved histidine residues.
Length = 192
Score = 26.5 bits (59), Expect = 3.4
Identities = 14/76 (18%), Positives = 24/76 (31%), Gaps = 8/76 (10%)
Query: 56 DPDDVGSVDFESFLKLMANH--IPNVDSTA---ELLEAFQVFDKDGEKLSDQEVDELIGL 110
DP E +LK + I N+ + L + + D V ++I
Sbjct: 37 DPFVKNGELLEDWLKEYNHGTLILNIKAEGLELRLKKLLAEYGITNYFFLDMSVPDIIKY 96
Query: 111 ADEN--NTGHVRYEEF 124
+ T R E+
Sbjct: 97 LENGEKRT-ATRVSEY 111
>gnl|CDD|236787 PRK10887, glmM, phosphoglucosamine mutase; Provisional.
Length = 443
Score = 27.0 bits (61), Expect = 3.6
Identities = 14/50 (28%), Positives = 18/50 (36%), Gaps = 15/50 (30%)
Query: 92 FDKDGEKLSD-------QEVDELIGLADENNTGHV--------RYEEFAK 126
F DG KL D E+D+ + + G RY EF K
Sbjct: 111 FSADGTKLPDEVELAIEAELDKPLTCVESAELGKASRINDAAGRYIEFCK 160
>gnl|CDD|100095 cd05802, GlmM, GlmM is a bacterial phosphoglucosamine mutase (PNGM)
that belongs to the alpha-D-phosphohexomutase
superfamily. It is required for the interconversion of
glucosamine-6-phosphate and glucosamine-1-phosphate in
the biosynthetic pathway of UDP-N-acetylglucosamine, an
essential precursor to components of the cell envelope.
In order to be active, GlmM must be phosphorylated,
which can occur via autophosphorylation or by the
Ser/Thr kinase StkP. GlmM functions in a classical
ping-pong bi-bi mechanism with
glucosamine-1,6-diphosphate as an intermediate. Other
members of the alpha-D-phosphohexomutase superfamily
include phosphoglucosamine mutase (PNGM),
phosphoacetylglucosamine mutase (PAGM), the bacterial
phosphomannomutase ManB, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 434
Score = 26.7 bits (60), Expect = 3.7
Identities = 14/52 (26%), Positives = 18/52 (34%), Gaps = 16/52 (30%)
Query: 91 VFDKDGEKLSDQEVDEL----------------IGLADENNTGHVRYEEFAK 126
F DG KL D+ +E+ IG + RY EF K
Sbjct: 108 FFSSDGYKLPDEVEEEIEALIDKELELPPTGEKIGRVYRIDDARGRYIEFLK 159
>gnl|CDD|221230 pfam11800, RP-C_C, Replication protein C C-terminal region.
Replication protein C is involved in the early stages
of viral DNA replication.
Length = 208
Score = 26.4 bits (59), Expect = 4.1
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 32 VGTVMRAIGRNPTEQELEDLLKE 54
++R + R T +LE LL E
Sbjct: 10 FRAIVRRLPRKATLADLEALLDE 32
>gnl|CDD|237794 PRK14705, PRK14705, glycogen branching enzyme; Provisional.
Length = 1224
Score = 26.9 bits (59), Expect = 4.2
Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 10/58 (17%)
Query: 14 EAFALFDKNGSGKIVSKYVGTVMR--------AIGRNPTEQELEDLLKEVDPDDVGSV 63
E D G ++ V +R A+G P + L++LL +D + G +
Sbjct: 276 ETLGTHDGQEQGPDIAAGVARRVRGSWAEAGPAVG--PYDHALDELLSALDGRNAGQL 331
>gnl|CDD|237870 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 491
Score = 26.7 bits (59), Expect = 4.4
Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 39 IGRNPTEQELEDLLKEVDPDDVGSVDFESFLKLMANHIPN-VDSTAELLEAFQVFDKDGE 97
+ + PT++ L + L ++ + D ES LKL+A + + + LLE ++ +
Sbjct: 172 LQKIPTDK-LVEHLVDIAKKENIEHDEES-LKLIAENSSGSMRNALFLLEQAAIYSNN-- 227
Query: 98 KLSDQEVDELIGLADEN 114
K+S++ V +L+G D++
Sbjct: 228 KISEKSVRDLLGCVDKH 244
>gnl|CDD|178005 PLN02379, PLN02379, pfkB-type carbohydrate kinase family protein.
Length = 367
Score = 26.7 bits (59), Expect = 4.5
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 44 TEQELEDLLKEVDPDDVGSVDFESFLKLMA 73
T +ELE +L+EV+ + S D S +K MA
Sbjct: 56 TIEELEHILREVNAHILPSPDDLSPIKTMA 85
>gnl|CDD|234854 PRK00881, purH, bifunctional
phosphoribosylaminoimidazolecarboxamide
formyltransferase/IMP cyclohydrolase; Provisional.
Length = 513
Score = 26.6 bits (60), Expect = 4.6
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 40 GRNPTEQELEDLL 52
R PTEQEL+DLL
Sbjct: 390 KRQPTEQELKDLL 402
>gnl|CDD|176201 cd08239, THR_DH_like, L-threonine dehydrogenase (TDH)-like.
MDR/AHD-like proteins, including a protein annotated as
a threonine dehydrogenase. L-threonine dehydrogenase
(TDH) catalyzes the zinc-dependent formation of
2-amino-3-ketobutyrate from L-threonine via
NAD(H)-dependent oxidation. The zinc-dependent alcohol
dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent
interconversion of alcohols to aldehydes or ketones.
Zinc-dependent ADHs are medium chain
dehydrogenase/reductase type proteins (MDRs) and have a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. In addition to alcohol
dehydrogenases, this group includes quinone reductase,
sorbitol dehydrogenase, formaldehyde dehydrogenase,
butanediol DH, ketose reductase, cinnamyl reductase, and
numerous others. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 339
Score = 26.5 bits (59), Expect = 4.9
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 14 EAFALFDKNGSGKIV 28
EA+ALF + SGK+V
Sbjct: 322 EAYALFAQGESGKVV 336
>gnl|CDD|234431 TIGR03990, Arch_GlmM, phosphoglucosamine mutase. The MMP1680
protein from Methanococcus maripaludis has been
characterized as the archaeal protein responsible for
the second step of UDP-GlcNAc biosynthesis. This GlmM
protein catalyzes the conversion of
glucosamine-6-phosphate to glucosamine-1-phosphate. The
first-characterized bacterial GlmM protein is modeled by
TIGR01455. These two families are members of the larger
phosphoglucomutase/phosphomannomutase family
(characterized by three domains: pfam02878, pfam02879
and pfam02880), but are not nearest neighbors to each
other. This model also includes a number of sequences
from non-archaea in the Bacteroides, Chlorobi,
Chloroflexi, Planctomycetes and Spirochaetes lineages.
Evidence supporting their inclusion in this equivalog as
having the same activity comes from genomic context and
phylogenetic profiling. A large number of these
organisms are known to produce exo-polysaccharide and
yet only appeared to contain the GlmS enzyme of the
GlmSMU pathway for UDP-GlcNAc biosynthesis
(GenProp0750). In some organisms including Leptospira,
this archaeal GlmM is found adjacent to the GlmS as well
as a putative GlmU non-orthologous homolog. Phylogenetic
profiling of the GlmS-only pattern using PPP identifies
members of this archaeal GlmM family as the
highest-scoring result [Central intermediary metabolism,
Amino sugars].
Length = 443
Score = 26.3 bits (59), Expect = 5.2
Identities = 8/40 (20%), Positives = 21/40 (52%)
Query: 88 AFQVFDKDGEKLSDQEVDELIGLADENNTGHVRYEEFAKV 127
++ + DG +LS ++ +E+ +A+ + ++E V
Sbjct: 103 GIKLLNSDGTELSREQEEEIEEIAESGDFERADWDEIGTV 142
>gnl|CDD|215491 PLN02906, PLN02906, xanthine dehydrogenase.
Length = 1319
Score = 26.2 bits (58), Expect = 5.9
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 9/43 (20%)
Query: 17 ALFDKNGS-------GKIVSKYVGTVMRAIGRNPTEQELEDLL 52
AL +GS G I+S Y ++R+ PTE+++E+ L
Sbjct: 81 ALASMHGSQCGFCTPGFIMSMY--ALLRSSKTPPTEEQIEECL 121
>gnl|CDD|236480 PRK09358, PRK09358, adenosine deaminase; Provisional.
Length = 340
Score = 25.9 bits (58), Expect = 6.7
Identities = 11/39 (28%), Positives = 14/39 (35%)
Query: 27 IVSKYVGTVMRAIGRNPTEQELEDLLKEVDPDDVGSVDF 65
I + + MR G +ELE L D V D
Sbjct: 134 ISVRLILCFMRHFGEEAAARELEALAARYRDDGVVGFDL 172
>gnl|CDD|107321 cd06326, PBP1_STKc_like, Type I periplasmic binding domain of
uncharacterized extracellular ligand-binding proteins.
The type I periplasmic binding domain of uncharacterized
extracellular ligand-binding proteins, some of which
contain a conserved catalytic serine/threonine protein
kinase (STKc) domain in the N-terminal region. Members
of this group are sequence-similar to the branched-chain
amino acid ABC transporter
leucine-isoleucine-valine-binding protein (LIVBP); their
ligand specificity has not been determined
experimentally, however.
Length = 336
Score = 26.0 bits (58), Expect = 6.8
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 25 GKIVSKYVGTVMRAIGRNPTEQELEDLLKEVDPDDVGS--VDF 65
G I +K + +R G +PT + L L+ + D+G +DF
Sbjct: 282 GYIAAKVLVEALRRAGPDPTRESLLAALEAMGKFDLGGFRLDF 324
>gnl|CDD|143266 cd05858, Ig3_FGFR-2, Third immunoglobulin (Ig)-like domain of
fibroblast growth factor receptor 2 (FGFR2).
Ig3_FGFR-2-like; domain similar to the third
immunoglobulin (Ig)-like domain of human fibroblast
growth factor receptor 2 (FGFR2). Fibroblast growth
factors (FGFs) participate in morphogenesis,
development, angiogenesis, and wound healing. These
FGF-stimulated processes are mediated by four FGFR
tyrosine kinases (FGRF1-4). FGFRs are comprised of an
extracellular portion consisting of three Ig-like
domains, a transmembrane helix, and a cytoplasmic
portion having protein tyrosine kinase activity. The
highly conserved Ig-like domains 2 and 3, and the
linker region between D2 and D3 define a general
binding site for FGFs. FGFR2 is required for male sex
determination.
Length = 90
Score = 24.9 bits (54), Expect = 7.5
Identities = 19/45 (42%), Positives = 27/45 (60%), Gaps = 4/45 (8%)
Query: 20 DKNGS--GKIVSKYVGTVMRAIGRNPTEQELEDL-LKEVDPDDVG 61
+KNGS G YV TV++ G N T++E+E L L+ V +D G
Sbjct: 25 EKNGSKYGPDGLPYV-TVLKTAGVNTTDKEMEVLYLRNVTFEDAG 68
>gnl|CDD|206142 pfam13972, TetR, Bacterial transcriptional repressor. This
family of bacterial transcriptional repressors is
characterized by the short approximately 50 amino acid
stretch of residues constituting the helix-turn-helix
DNA binding motif, around the YRFhY motif. The target
proteins that are repressed are involved in the
transcriptional control of multi-drug efflux pumps,
pathways for the biosynthesis of antibiotics, response
to osmotic stress and toxic chemicals, control of
catabolic pathways, differentiation processes, and
pathogenicity. The regulatory network in which TetR
itself is involved is in being released in the presence
of tetracycline, binding to the target operator, and
repressing tetA transcription.
Length = 146
Score = 25.3 bits (56), Expect = 8.0
Identities = 9/32 (28%), Positives = 15/32 (46%)
Query: 45 EQELEDLLKEVDPDDVGSVDFESFLKLMANHI 76
EQEL +LL + + D +L L+ +
Sbjct: 4 EQELLELLAPPEGRPLTLEDLWLYLDLLFELM 35
>gnl|CDD|234945 PRK01346, PRK01346, hypothetical protein; Provisional.
Length = 411
Score = 25.7 bits (57), Expect = 8.2
Identities = 8/30 (26%), Positives = 14/30 (46%)
Query: 30 KYVGTVMRAIGRNPTEQELEDLLKEVDPDD 59
+ G +P+++ELE V+PD
Sbjct: 19 AWFRAAATGFGDSPSDEELEAWRALVEPDR 48
>gnl|CDD|130522 TIGR01455, glmM, phosphoglucosamine mutase. This model describes
GlmM, phosphoglucosamine mutase, also designated in MrsA
and YhbF E. coli, UreC in Helicobacter pylori, and
femR315 or FemD in Staphlococcus aureus. It converts
glucosamine-6-phosphate to glucosamine-1-phosphate as
part of the pathway toward UDP-N-acetylglucosamine for
peptidoglycan and lipopolysaccharides [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan, Central intermediary metabolism, Amino
sugars].
Length = 443
Score = 25.8 bits (57), Expect = 8.3
Identities = 13/52 (25%), Positives = 15/52 (28%), Gaps = 17/52 (32%)
Query: 92 FDKDGEKLSDQEVDELIGLADENNTG-----------------HVRYEEFAK 126
F G KL D + L DE + RY EF K
Sbjct: 110 FGPGGFKLDDATEAAIEALLDEADPLPRPESEGLGRVKRYPDAVGRYIEFLK 161
>gnl|CDD|238992 cd02035, ArsA, ArsA ATPase functionas as an efflux pump located on
the inner membrane of the cell. This ATP-driven oxyanion
pump catalyzes the extrusion of arsenite, antimonite and
arsenate. Maintenance of a low intracellular
concentration of oxyanion produces resistance to the
toxic agents. The pump is composed of two subunits, the
catalytic ArsA subunit and the membrane subunit ArsB,
which are encoded by arsA and arsB genes respectively.
Arsenic efflux in bacteria is catalyzed by either ArsB
alone or by ArsAB complex. The ATP-coupled pump,
however, is more efficient. ArsA is composed of two
homologous halves, A1 and A2, connected by a short
linker sequence.
Length = 217
Score = 25.7 bits (57), Expect = 8.8
Identities = 10/64 (15%), Positives = 18/64 (28%), Gaps = 6/64 (9%)
Query: 38 AIGRNPTEQELEDLLKEVDPDDVGSVDFE---SFLKLMANHIPNVD---STAELLEAFQV 91
A E +EVD + + +A +P ++ S + F
Sbjct: 52 AFIVEDPEIAPNLYREEVDATRRVERAWGGEGGLMLELAAALPGIEELASLLAVFREFSE 111
Query: 92 FDKD 95
D
Sbjct: 112 GLYD 115
>gnl|CDD|214822 smart00798, AICARFT_IMPCHas, AICARFT/IMPCHase bienzyme. This is a
family of bifunctional enzymes catalysing the last two
steps in de novo purine biosynthesis. The bifunctional
enzyme is found in both prokaryotes and eukaryotes. The
second last step is catalysed by
5-aminoimidazole-4-carboxamide ribonucleotide
formyltransferase (AICARFT), this enzyme catalyses the
formylation of AICAR with 10-formyl-tetrahydrofolate to
yield FAICAR and tetrahydrofolate. The last step is
catalysed by IMP (Inosine monophosphate) cyclohydrolase
(IMPCHase), cyclizing FAICAR
(5-formylaminoimidazole-4-carboxamide ribonucleotide) to
IMP.
Length = 311
Score = 25.5 bits (57), Expect = 9.0
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 10/27 (37%)
Query: 26 KIVSKYVGTVMRAIGRNPTEQELEDLL 52
K+V+K R PTE+EL DLL
Sbjct: 252 KVVTK----------RQPTEEELADLL 268
>gnl|CDD|99746 cd06453, SufS_like, Cysteine desulfurase (SufS)-like. This family
belongs to the pyridoxal phosphate (PLP)-dependent
aspartate aminotransferase superfamily (fold I). The
major groups in this CD correspond to cysteine
desulfurase (SufS) and selenocysteine lyase. SufS
catalyzes the removal of elemental sulfur and selenium
atoms from L-cysteine, L-cystine, L-selenocysteine, and
L-selenocystine to produce L-alanine; and selenocysteine
lyase catalyzes the decomposition of L-selenocysteine.
Length = 373
Score = 25.5 bits (57), Expect = 9.4
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 8/36 (22%)
Query: 52 LKEVDPDDVGSVDFESFLKLMA--------NHIPNV 79
LK V DD G +D E+ KL+ H+ NV
Sbjct: 116 LKVVPVDDDGQLDLEALEKLLTERTKLVAVTHVSNV 151
>gnl|CDD|173964 cd07981, TAF12, TATA Binding Protein (TBP) Associated Factor 12
(TAF12) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 12 (TAF12) is one of several TAFs that bind TBP
and are involved in forming the TFIID complex. TFIID is
one of the seven General Transcription Factors (GTFs)
(TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are
involved in accurate initiation of transcription by RNA
polymerase II in eukaryotes. TFIID plays an important
role in the recognition of promoter DNA and assembly of
the pre-initiation complex. TFIID complex is composed
of the TBP and at least 13 TAFs. TAFs are named after
their electrophoretic mobility in polyacrylamide gels
in different species. A new, unified nomenclature has
been suggested for the pol II TAFs to show the
relationship between TAF orthologs and paralogs.
Several hypotheses are proposed for TAFs function such
as serving as activator-binding sites, core-promoter
recognition or a role in essential catalytic activity.
These TAFs, with the help of specific activators, are
required only for expression of a subset of genes and
are not universally involved for transcription as are
GTFs. In yeast and human cells, TAFs have been found as
components of other complexes besides TFIID. Several
TAFs interact via histone-fold (HFD) motifs; the HFD is
the interaction motif involved in heterodimerization of
the core histones and their assembly into nucleosome
octamers. The minimal HFD contains three alpha-helices
linked by two loops and is found in core histones, TAFs
and many other transcription factors. TFIID has a
histone octamer-like substructure. TAF12 domain
interacts with TAF4 and makes a novel histone-like
heterodimer that binds DNA and has a core promoter
function of a subset of genes.
Length = 72
Score = 24.5 bits (54), Expect = 9.5
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 43 PTEQELEDLLKEVDPDDVGSVDFESFLKLMAN 74
T+++L++LLKE+DP + D E L +A+
Sbjct: 2 LTKRKLQELLKEIDPREQLDPDVEELLLEIAD 33
>gnl|CDD|216850 pfam02020, W2, eIF4-gamma/eIF5/eIF2-epsilon. This domain of
unknown function is found at the C-terminus of several
translation initiation factors.
Length = 75
Score = 24.5 bits (54), Expect = 9.6
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 4 LDEEQITEWKEAFALFDKNGSGKIVSK 30
L+EE I +W E D GS K+ +
Sbjct: 38 LEEEAILKWYEKSKKVDGEGSKKVRKQ 64
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.312 0.133 0.365
Gapped
Lambda K H
0.267 0.0827 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,042,580
Number of extensions: 651794
Number of successful extensions: 962
Number of sequences better than 10.0: 1
Number of HSP's gapped: 942
Number of HSP's successfully gapped: 127
Length of query: 131
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 45
Effective length of database: 7,123,158
Effective search space: 320542110
Effective search space used: 320542110
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (24.0 bits)