RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12851
(148 letters)
>gnl|CDD|185504 PTZ00184, PTZ00184, calmodulin; Provisional.
Length = 149
Score = 205 bits (523), Expect = 3e-69
Identities = 98/148 (66%), Positives = 121/148 (81%)
Query: 1 MADQLTEEQINDFKEAFSFFNRQGDGRIPIHELGTVMRFLGLTPTEAELLDLIREIDVNQ 60
MADQLTEEQI +FKEAFS F++ GDG I ELGTVMR LG PTEAEL D+I E+D +
Sbjct: 1 MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 60
Query: 61 RGTIDFPEFLTVMARKLNTPDSTEEIKQAFQVFDKHKQGYICADELRHVMTTLGERLSED 120
GTIDFPEFLT+MARK+ DS EEIK+AF+VFD+ G+I A ELRHVMT LGE+L+++
Sbjct: 61 NGTIDFPEFLTLMARKMKDTDSEEEIKEAFKVFDRDGNGFISAAELRHVMTNLGEKLTDE 120
Query: 121 EVNEMIQEADINGDGRINYEDFVTLMTS 148
EV+EMI+EAD++GDG+INYE+FV +M S
Sbjct: 121 EVDEMIREADVDGDGQINYEEFVKMMMS 148
Score = 54.4 bits (131), Expect = 4e-10
Identities = 33/76 (43%), Positives = 46/76 (60%), Gaps = 3/76 (3%)
Query: 1 MADQLTEEQINDFKEAFSFFNRQGDGRIPIHELGTVMRFLGLTPTEAELLDLIREIDVNQ 60
M D +EE+I KEAF F+R G+G I EL VM LG T+ E+ ++IRE DV+
Sbjct: 77 MKDTDSEEEI---KEAFKVFDRDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADVDG 133
Query: 61 RGTIDFPEFLTVMARK 76
G I++ EF+ +M K
Sbjct: 134 DGQINYEEFVKMMMSK 149
>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 = 159 bits (405), Expect = 4e-51
Identities = 75/145 (51%), Positives = 101/145 (69%), Gaps = 1/145 (0%)
Query: 4 QLTEEQINDFKEAFSFFNRQGDGRIPIHELGTVMRFLGLTPTEAELLDLIREIDVNQRGT 63
QLTEEQI + KEAF F+R DG I +ELG ++R LG P+EAE+ L EID T
Sbjct: 13 QLTEEQIQELKEAFQLFDRDSDGLIDRNELGKILRSLGFNPSEAEINKLFEEIDAG-NET 71
Query: 64 IDFPEFLTVMARKLNTPDSTEEIKQAFQVFDKHKQGYICADELRHVMTTLGERLSEDEVN 123
+DFPEFLTVM+ KL D EE+++AF++FDK GYI ELR V+ +LGERLS++EV
Sbjct: 72 VDFPEFLTVMSVKLKRGDKEEELREAFKLFDKDHDGYISIGELRRVLKSLGERLSDEEVE 131
Query: 124 EMIQEADINGDGRINYEDFVTLMTS 148
++++E D +GDG I+YE+F L+
Sbjct: 132 KLLKEYDEDGDGEIDYEEFKKLIKD 156
Score = 49.2 bits (118), Expect = 4e-08
Identities = 22/66 (33%), Positives = 37/66 (56%)
Query: 11 NDFKEAFSFFNRQGDGRIPIHELGTVMRFLGLTPTEAELLDLIREIDVNQRGTIDFPEFL 70
+ +EAF F++ DG I I EL V++ LG ++ E+ L++E D + G ID+ EF
Sbjct: 92 EELREAFKLFDKDHDGYISIGELRRVLKSLGERLSDEEVEKLLKEYDEDGDGEIDYEEFK 151
Query: 71 TVMARK 76
++
Sbjct: 152 KLIKDS 157
>gnl|CDD|185503 PTZ00183, PTZ00183, centrin; Provisional.
Length = 158
Score = 128 bits (323), Expect = 1e-38
Identities = 62/144 (43%), Positives = 86/144 (59%)
Query: 4 QLTEEQINDFKEAFSFFNRQGDGRIPIHELGTVMRFLGLTPTEAELLDLIREIDVNQRGT 63
LTE+Q + +EAF F+ G G I EL MR LG P + E+ +I ++D + G
Sbjct: 10 GLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGFEPKKEEIKQMIADVDKDGSGK 69
Query: 64 IDFPEFLTVMARKLNTPDSTEEIKQAFQVFDKHKQGYICADELRHVMTTLGERLSEDEVN 123
IDF EFL +M +KL D EEI +AF++FD K G I L+ V LGE ++++E+
Sbjct: 70 IDFEEFLDIMTKKLGERDPREEILKAFRLFDDDKTGKISLKNLKRVAKELGETITDEELQ 129
Query: 124 EMIQEADINGDGRINYEDFVTLMT 147
EMI EAD NGDG I+ E+F +M
Sbjct: 130 EMIDEADRNGDGEISEEEFYRIMK 153
Score = 57.0 bits (138), Expect = 4e-11
Identities = 26/70 (37%), Positives = 44/70 (62%)
Query: 79 TPDSTEEIKQAFQVFDKHKQGYICADELRHVMTTLGERLSEDEVNEMIQEADINGDGRIN 138
T D +EI++AF +FD G I EL+ M +LG ++E+ +MI + D +G G+I+
Sbjct: 12 TEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGFEPKKEEIKQMIADVDKDGSGKID 71
Query: 139 YEDFVTLMTS 148
+E+F+ +MT
Sbjct: 72 FEEFLDIMTK 81
Score = 42.8 bits (101), Expect = 1e-05
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 1 MADQLTEEQINDFKEAFSFFNRQGDGRIPIHELGTVMRFLGLTPTEAELLDLIREIDVNQ 60
+ ++ E+I +AF F+ G+I + L V + LG T T+ EL ++I E D N
Sbjct: 83 LGERDPREEIL---KAFRLFDDDKTGKISLKNLKRVAKELGETITDEELQEMIDEADRNG 139
Query: 61 RGTIDFPEFLTVMARK 76
G I EF +M +
Sbjct: 140 DGEISEEEFYRIMKKT 155
>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 = 72.2 bits (178), Expect = 8e-18
Identities = 32/63 (50%), Positives = 50/63 (79%)
Query: 85 EIKQAFQVFDKHKQGYICADELRHVMTTLGERLSEDEVNEMIQEADINGDGRINYEDFVT 144
E+++AF++FDK G I ADEL+ + +LGE LSE+E++EMI+E D +GDG+I++E+F+
Sbjct: 1 ELREAFRLFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLE 60
Query: 145 LMT 147
LM
Sbjct: 61 LMA 63
Score = 55.2 bits (134), Expect = 3e-11
Identities = 27/63 (42%), Positives = 40/63 (63%)
Query: 12 DFKEAFSFFNRQGDGRIPIHELGTVMRFLGLTPTEAELLDLIREIDVNQRGTIDFPEFLT 71
+ +EAF F++ GDG I EL ++ LG +E E+ ++IRE+D + G IDF EFL
Sbjct: 1 ELREAFRLFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLE 60
Query: 72 VMA 74
+MA
Sbjct: 61 LMA 63
Score = 43.3 bits (103), Expect = 1e-06
Identities = 19/64 (29%), Positives = 27/64 (42%), Gaps = 1/64 (1%)
Query: 48 ELLDLIREIDVNQRGTIDFPEFLTVMARKLNTPDSTEEIKQAFQVFDKHKQGYICADELR 107
EL + R D + GTI E + + L S EEI + + DK G I +E
Sbjct: 1 ELREAFRLFDKDGDGTISADELKAAL-KSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFL 59
Query: 108 HVMT 111
+M
Sbjct: 60 ELMA 63
>gnl|CDD|222407 pfam13833, EF_hand_6, EF-hand domain pair.
Length = 53
Score = 53.7 bits (130), Expect = 7e-11
Identities = 20/52 (38%), Positives = 35/52 (67%)
Query: 97 KQGYICADELRHVMTTLGERLSEDEVNEMIQEADINGDGRINYEDFVTLMTS 148
++G I +EL+ + LG LSE+EV+ + +E D +GDG+I++E+F L+
Sbjct: 1 EKGLITREELKRALALLGISLSEEEVDILFREFDTDGDGKISFEEFCVLLQR 52
Score = 37.5 bits (88), Expect = 1e-04
Identities = 18/53 (33%), Positives = 26/53 (49%)
Query: 24 GDGRIPIHELGTVMRFLGLTPTEAELLDLIREIDVNQRGTIDFPEFLTVMARK 76
G I EL + LG++ +E E+ L RE D + G I F EF ++ R
Sbjct: 1 EKGLITREELKRALALLGISLSEEEVDILFREFDTDGDGKISFEEFCVLLQRL 53
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 52.4 bits (126), Expect = 3e-10
Identities = 24/60 (40%), Positives = 40/60 (66%), Gaps = 4/60 (6%)
Query: 91 QVFDKHKQGYICADELRHVMTTLGERLSEDEVNEMIQE----ADINGDGRINYEDFVTLM 146
++ DK GYI +ELR ++ LG +L+++EV E+I+ D +GDGRI++E+F+ M
Sbjct: 1 KLLDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEFLEAM 60
Score = 38.1 bits (89), Expect = 7e-05
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 20 FNRQGDGRIPIHELGTVMRFLGLTPTEAELLDLIREI----DVNQRGTIDFPEFLTVM 73
++ GDG I + EL +++ LGL T+ E+ +LI D + G I F EFL M
Sbjct: 3 LDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEFLEAM 60
Score = 30.4 bits (69), Expect = 0.053
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 3/60 (5%)
Query: 54 REIDVNQRGTI---DFPEFLTVMARKLNTPDSTEEIKQAFQVFDKHKQGYICADELRHVM 110
+ +D + G I + + L + KL + E I+ F DK G I +E M
Sbjct: 1 KLLDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEFLEAM 60
Score = 24.2 bits (53), Expect = 9.5
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 127 QEADINGDGRINYEDFVTLMTS 148
+ D +GDG I+ E+ L+ +
Sbjct: 1 KLLDKDGDGYIDVEELRKLLKA 22
>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 = 42.6 bits (101), Expect = 2e-06
Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 86 IKQAFQVFDKHKQGYICADELRHVMTTLGERLSEDEVNEMIQEADINGDGRINYEDFVTL 145
Q F+ D G I DE R + G L + ++ AD + DG+++ E+F
Sbjct: 1 YDQIFRSLDPDGDGLISGDEARPFLGKSG--LPRSVLAQIWDLADTDKDGKLDKEEFAIA 58
Query: 146 M 146
M
Sbjct: 59 M 59
Score = 32.2 bits (74), Expect = 0.013
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 4/65 (6%)
Query: 13 FKEAFSFFNRQGDGRIPIHELGTVMRFLGLTPTEAELLDLIREIDVNQRGTIDFPEFLTV 72
+ + F + GDG I E + GL + L + D ++ G +D EF
Sbjct: 1 YDQIFRSLDPDGDGLISGDEARPFLGKSGLPRSV--LAQIWDLADTDKDGKLDKEEF--A 56
Query: 73 MARKL 77
+A L
Sbjct: 57 IAMHL 61
>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 = 38.1 bits (90), Expect = 4e-05
Identities = 10/28 (35%), Positives = 19/28 (67%)
Query: 121 EVNEMIQEADINGDGRINYEDFVTLMTS 148
E+ E + D +GDG+I++E+F L+ +
Sbjct: 1 ELKEAFRLFDKDGDGKIDFEEFKDLLKA 28
Score = 31.2 bits (72), Expect = 0.017
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 85 EIKQAFQVFDKHKQGYICADELRHVMTTL 113
E+K+AF++FDK G I +E + ++ L
Sbjct: 1 ELKEAFRLFDKDGDGKIDFEEFKDLLKAL 29
Score = 31.2 bits (72), Expect = 0.018
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 48 ELLDLIREIDVNQRGTIDFPEFLTVMARK 76
EL + R D + G IDF EF ++
Sbjct: 1 ELKEAFRLFDKDGDGKIDFEEFKDLLKAL 29
Score = 24.6 bits (55), Expect = 3.4
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 12 DFKEAFSFFNRQGDGRIPIHELGTVMR 38
+ KEAF F++ GDG+I E +++
Sbjct: 1 ELKEAFRLFDKDGDGKIDFEEFKDLLK 27
>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 = 37.0 bits (87), Expect = 1e-04
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 121 EVNEMIQEADINGDGRINYEDFVTLMTS 148
E+ E +E D +GDG+I++E+F L+
Sbjct: 1 ELKEAFKEFDKDGDGKISFEEFKELLKK 28
Score = 32.8 bits (76), Expect = 0.004
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 85 EIKQAFQVFDKHKQGYICADELRHVMTTL 113
E+K+AF+ FDK G I +E + ++ L
Sbjct: 1 ELKEAFKEFDKDGDGKISFEEFKELLKKL 29
Score = 30.9 bits (71), Expect = 0.022
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 48 ELLDLIREIDVNQRGTIDFPEFLTVMAR 75
EL + +E D + G I F EF ++ +
Sbjct: 1 ELKEAFKEFDKDGDGKISFEEFKELLKK 28
Score = 25.1 bits (56), Expect = 2.5
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 12 DFKEAFSFFNRQGDGRIPIHELGTVMR 38
+ KEAF F++ GDG+I E +++
Sbjct: 1 ELKEAFKEFDKDGDGKISFEEFKELLK 27
>gnl|CDD|205583 pfam13405, EF_hand_4, EF-hand domain.
Length = 30
Score = 36.4 bits (85), Expect = 2e-04
Identities = 15/30 (50%), Positives = 23/30 (76%)
Query: 85 EIKQAFQVFDKHKQGYICADELRHVMTTLG 114
E+++AF++FDK GYI A+ELR + +LG
Sbjct: 1 ELREAFKLFDKDGDGYISAEELRKALRSLG 30
Score = 31.0 bits (71), Expect = 0.017
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 12 DFKEAFSFFNRQGDGRIPIHELGTVMRFLG 41
+ +EAF F++ GDG I EL +R LG
Sbjct: 1 ELREAFKLFDKDGDGYISAEELRKALRSLG 30
Score = 24.5 bits (54), Expect = 4.2
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 121 EVNEMIQEADINGDGRINYEDFVTLMTS 148
E+ E + D +GDG I+ E+ + S
Sbjct: 1 ELREAFKLFDKDGDGYISAEELRKALRS 28
>gnl|CDD|238131 cd00213, S-100, S-100: S-100 domain, which represents the largest
family within the superfamily of proteins carrying the
Ca-binding EF-hand motif. Note that this S-100 hierarchy
contains only S-100 EF-hand domains, other EF-hands have
been modeled separately. S100 proteins are expressed
exclusively in vertebrates, and are implicated in
intracellular and extracellular regulatory activities.
Intracellularly, S100 proteins act as Ca-signaling or
Ca-buffering proteins. The most unusual characteristic
of certain S100 proteins is their occurrence in
extracellular space, where they act in a cytokine-like
manner through RAGE, the receptor for advanced glycation
products. Structural data suggest that many S100 members
exist within cells as homo- or heterodimers and even
oligomers; oligomerization contributes to their
functional diversification. Upon binding calcium, most
S100 proteins change conformation to a more open
structure exposing a hydrophobic cleft. This hydrophobic
surface represents the interaction site of S100 proteins
with their target proteins. There is experimental
evidence showing that many S100 proteins have multiple
binding partners with diverse mode of interaction with
different targets. In addition to S100 proteins (such as
S100A1,-3,-4,-6,-7,-10,-11,and -13), this group includes
the ''fused'' gene family, a group of calcium binding
S100-related proteins. The ''fused'' gene family
includes multifunctional epidermal differentiation
proteins - profilaggrin, trichohyalin, repetin,
hornerin, and cornulin; functionally these proteins are
associated with keratin intermediate filaments and
partially crosslinked to the cell envelope. These
''fused'' gene proteins contain N-terminal sequence with
two Ca-binding EF-hands motif, which may be associated
with calcium signaling in epidermal cells and
autoprocessing in a calcium-dependent manner. In
contrast to S100 proteins, "fused" gene family proteins
contain an extraordinary high number of almost perfect
peptide repeats with regular array of polar and charged
residues similar to many known cell envelope proteins.
Length = 88
Score = 34.0 bits (79), Expect = 0.005
Identities = 9/45 (20%), Positives = 28/45 (62%), Gaps = 3/45 (6%)
Query: 104 DELRHVMTTLGERLSEDEVNEMIQEADINGDGRINYEDFVTLMTS 148
EL + + + + V++++++ D+N DG++++++F+ L+
Sbjct: 38 TELPNFLKNQKD---PEAVDKIMKDLDVNKDGKVDFQEFLVLIGK 79
Score = 28.6 bits (65), Expect = 0.41
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 32 ELGTVMRFLGLTPTEAELLDLIREIDVNQRGTIDFPEFLTVMAR 75
EL FL + +++++DVN+ G +DF EFL ++ +
Sbjct: 39 ELPN---FLKNQKDPEAVDKIMKDLDVNKDGKVDFQEFLVLIGK 79
>gnl|CDD|215520 PLN02964, PLN02964, phosphatidylserine decarboxylase.
Length = 644
Score = 35.6 bits (82), Expect = 0.006
Identities = 15/69 (21%), Positives = 33/69 (47%), Gaps = 2/69 (2%)
Query: 80 PDSTEE--IKQAFQVFDKHKQGYICADELRHVMTTLGERLSEDEVNEMIQEADINGDGRI 137
P TE ++ + D + G + E ++ G ++ ++ E+ + AD+NGDG +
Sbjct: 173 PVETERSFARRILAIVDYDEDGQLSFSEFSDLIKAFGNLVAANKKEELFKAADLNGDGVV 232
Query: 138 NYEDFVTLM 146
++ L+
Sbjct: 233 TIDELAALL 241
>gnl|CDD|193239 pfam12763, efhand_3, Cytoskeletal-regulatory complex EF hand. This
is an efhand family from the N-terminal of actin
cytoskeleton-regulatory complex END3 and similar
proteins from fungi and closely related species.
Length = 104
Score = 33.5 bits (77), Expect = 0.008
Identities = 18/64 (28%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 85 EIKQAFQVFD--KHKQGYICADELRHVMTTLGERLSEDEVNEMIQEADINGDGRINYEDF 142
EIK+ +++F K + + D++ V+ RL +D++ ++ ADI+ DG++++E+F
Sbjct: 8 EIKKYWEIFSGLKPENNKLTGDQVSPVLKN--SRLPDDQLAKIWDLADIDSDGKLDFEEF 65
Query: 143 VTLM 146
M
Sbjct: 66 CIAM 69
>gnl|CDD|197477 smart00027, EH, Eps15 homology domain. Pair of EF hand motifs that
recognise proteins containing Asn-Pro-Phe (NPF)
sequences.
Length = 96
Score = 33.0 bits (76), Expect = 0.012
Identities = 16/68 (23%), Positives = 35/68 (51%), Gaps = 5/68 (7%)
Query: 82 STEEIKQAFQVF---DKHKQGYICADELRHVMTTLGERLSEDEVNEMIQEADINGDGRIN 138
S E+ + Q+F DK++ G + + + ++ G L + + ++ ADI+ DG ++
Sbjct: 5 SPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSG--LPQTLLAKIWNLADIDNDGELD 62
Query: 139 YEDFVTLM 146
++F M
Sbjct: 63 KDEFALAM 70
Score = 29.2 bits (66), Expect = 0.29
Identities = 19/86 (22%), Positives = 37/86 (43%), Gaps = 7/86 (8%)
Query: 5 LTEEQINDFKEAFSFFNRQGDGRIPIHELGTVMRFLGLTPTE-AELLDLIREIDVNQRGT 63
++ E +++ F ++ DG + + ++ GL T A++ +L D++ G
Sbjct: 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWNLA---DIDNDGE 60
Query: 64 IDFPEFLTVM---ARKLNTPDSTEEI 86
+D EF M RKLN +
Sbjct: 61 LDKDEFALAMHLIYRKLNGYPIPASL 86
>gnl|CDD|240156 cd05030, calgranulins, Calgranulins: S-100 domain found in proteins
belonging to the Calgranulin subgroup of the S100 family
of EF-hand calcium-modulated proteins, including S100A8,
S100A9, and S100A12 . Note that the S-100 hierarchy, to
which this Calgranulin group belongs, contains only
S-100 EF-hand domains, other EF-hands have been modeled
separately. These proteins are expressed mainly in
granulocytes, and are involved in inflammation, allergy,
and neuritogenesis, as well as in host-parasite
response. Calgranulins are modulated not only by
calcium, but also by other metals such as zinc and
copper. Structural data suggested that calgranulins may
exist in multiple structural forms, homodimers, as well
as hetero-oligomers. For example, the S100A8/S100A9
complex called calprotectin plays important roles in the
regulation of inflammatory processes, wound repair, and
regulating zinc-dependent enzymes as well as microbial
growth.
Length = 88
Score = 30.4 bits (69), Expect = 0.11
Identities = 7/26 (26%), Positives = 20/26 (76%)
Query: 122 VNEMIQEADINGDGRINYEDFVTLMT 147
++++ ++ D N DG++++E+F+ L+
Sbjct: 53 IDKIFEDLDTNQDGQLSFEEFLVLVI 78
Score = 28.9 bits (65), Expect = 0.32
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 39 FLGLTPTEAELLDLIREIDVNQRGTIDFPEFLTVMAR 75
FL + + + ++D NQ G + F EFL ++ +
Sbjct: 43 FLKKEKNQKAIDKIFEDLDTNQDGQLSFEEFLVLVIK 79
>gnl|CDD|240157 cd05031, S-100A10_like, S-100A10_like: S-100A10 domain found in
proteins similar to S100A10. S100A10 is a member of the
S100 family of EF-hand superfamily of calcium-binding
proteins. Note that the S-100 hierarchy, to which this
S-100A1_like group belongs, contains only S-100 EF-hand
domains, other EF-hands have been modeled separately.
S100 proteins are expressed exclusively in vertebrates,
and are implicated in intracellular and extracellular
regulatory activities. A unique feature of S100A10 is
that it contains mutation in both of the calcium binding
sites, making it calcium insensitive. S100A10 has been
detected in brain, heart, gastrointestinal tract,
kidney, liver, lung, spleen, testes, epidermis, aorta,
and thymus. Structural data supports the homo- and
hetero-dimeric as well as hetero-tetrameric nature of
the protein. S100A10 has multiple binding partners in
its calcium free state and is therefore involved in many
diverse biological functions.
Length = 94
Score = 29.3 bits (66), Expect = 0.26
Identities = 16/53 (30%), Positives = 32/53 (60%), Gaps = 5/53 (9%)
Query: 99 GYICADELRHVM-TTLGERLSEDE----VNEMIQEADINGDGRINYEDFVTLM 146
+ EL+ +M L E L + V++++++ D N DG++N+E+FV+L+
Sbjct: 25 NTLSRKELKKLMEKELSEFLKNQKDPMAVDKIMKDLDQNRDGKVNFEEFVSLV 77
>gnl|CDD|200457 cd11318, AmyAc_bac_fung_AmyA, Alpha amylase catalytic domain found
in bacterial and fungal Alpha amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes bacterial and fungal proteins. 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 = 391
Score = 30.6 bits (70), Expect = 0.27
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 13/59 (22%)
Query: 45 TEAELLDLIRE-----IDV------NQRGTIDFPEFLTVMARKLNTPDSTEEIKQAFQV 92
T+ ELL+ I+ I V N + D E TV A +++ D +EI + +++
Sbjct: 77 TKEELLEAIKALHENGIQVYADAVLNHKAGADETE--TVKAVEVDPNDRNKEISEPYEI 133
>gnl|CDD|240155 cd05029, S-100A6, S-100A6: S-100A6 domain found in proteins similar
to S100A6. S100A6 is a member of the S100 domain family
within EF-hand Ca2+-binding proteins superfamily. Note
that the S-100 hierarchy, to which this S-100A6 group
belongs, contains only S-100 EF-hand domains, other
EF-hands have been modeled separately. S100 proteins
exhibit unique patterns of tissue- and cell
type-specific expression and have been implicated in the
Ca2+-dependent regulation of diverse physiological
processes, including cell cycle regulation,
differentiation, growth, and metabolic control . S100A6
is normally expressed in the G1 phase of the cell cycle
in neuronal cells. The function of S100A6 remains
unclear, but evidence suggests that it is involved in
cell cycle regulation and exocytosis. S100A6 may also be
involved in tumorigenesis; the protein is overexpressed
in several tumors. Ca2+ binding to S100A6 leads to a
conformational change in the protein, which exposes a
hydrophobic surface for interaction with target
proteins. Several such proteins have been identified:
glyceraldehyde-3-phosphate dehydrogenase , annexins 2,
6 and 11 and Calcyclin-Binding Protein (CacyBP).
Length = 88
Score = 29.0 bits (65), Expect = 0.36
Identities = 14/53 (26%), Positives = 30/53 (56%)
Query: 94 DKHKQGYICADELRHVMTTLGERLSEDEVNEMIQEADINGDGRINYEDFVTLM 146
DK+ EL T+G +L + E+ +++++ D N D +N++++VT +
Sbjct: 25 DKNTLSKKELKELIQKELTIGSKLQDAEIAKLMEDLDRNKDQEVNFQEYVTFL 77
>gnl|CDD|205383 pfam13202, EF_hand_3, EF hand.
Length = 25
Score = 26.9 bits (61), Expect = 0.51
Identities = 8/25 (32%), Positives = 17/25 (68%)
Query: 122 VNEMIQEADINGDGRINYEDFVTLM 146
+ ++ ++ D NGDG+I+ E+ L+
Sbjct: 1 LKDLFRQFDTNGDGKISKEELKRLL 25
Score = 26.9 bits (61), Expect = 0.63
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 86 IKQAFQVFDKHKQGYICADELRHVM 110
+K F+ FD + G I +EL+ ++
Sbjct: 1 LKDLFRQFDTNGDGKISKEELKRLL 25
Score = 24.5 bits (55), Expect = 4.5
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 51 DLIREIDVNQRGTIDFPEFLTVM 73
DL R+ D N G I E ++
Sbjct: 3 DLFRQFDTNGDGKISKEELKRLL 25
>gnl|CDD|236035 PRK07508, PRK07508, aminodeoxychorismate synthase; Provisional.
Length = 378
Score = 29.6 bits (67), Expect = 0.57
Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 19 FFNRQGDGRIPIHEL-GTVMRFLGLTPTE-AELLDLIREIDVNQ 60
FF G+G I H + GT R G TP E A L + + NQ
Sbjct: 181 FFRVDGEGWIETHPMKGTAPR--GATPAEDARLRAALLNDEKNQ 222
>gnl|CDD|217775 pfam03874, RNA_pol_Rpb4, RNA polymerase Rpb4. This family includes
the Rpb4 protein. This family also includes C17 (aka
CGRP-RCP) is an essential subunit of RNA polymerase III.
C17 forms a subcomplex with C25 which is likely to be
the counterpart of subcomplex Rpb4/7 in Pol II.
Length = 110
Score = 28.7 bits (65), Expect = 0.62
Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 8/61 (13%)
Query: 76 KLNTPDSTEEIKQAFQVFDKHKQ-----GYIC---ADELRHVMTTLGERLSEDEVNEMIQ 127
+L P+S E+ + + F+ K + ADELR ++ +L R SE+++ E++
Sbjct: 45 RLKNPESARELVEELKEFELTKFEALQIVNLLPETADELRAIIESLESRFSEEQLEEILD 104
Query: 128 E 128
Sbjct: 105 I 105
>gnl|CDD|117964 pfam09424, YqeY, Yqey-like protein. The function of this domain
found in the YqeY protein is uncertain.
Length = 143
Score = 28.3 bits (64), Expect = 0.98
Identities = 20/83 (24%), Positives = 43/83 (51%), Gaps = 15/83 (18%)
Query: 53 IREIDVNQRGTIDFPEFLTVMARKLNTPDSTEEIKQ---AFQVFDKHKQGYICA---DEL 106
I++ +V++R + E LTV+A+ E+KQ + + F+K + + E+
Sbjct: 30 IKQEEVDERIELSDEEVLTVLAK---------EVKQRRESIEQFEKAGRQDLAEKEKAEI 80
Query: 107 RHVMTTLGERLSEDEVNEMIQEA 129
+ L ++LS++E+ ++ EA
Sbjct: 81 AILEEYLPQQLSDEEIEALVDEA 103
>gnl|CDD|220446 pfam09860, DUF2087, Uncharacterized protein conserved in bacteria
(DUF2087). This domain, found in various hypothetical
prokaryotic proteins and transcriptional activators, has
no known function. Structural modelling suggests this
domain may bind nucleic acids.
Length = 71
Score = 26.7 bits (60), Expect = 1.5
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 14/54 (25%)
Query: 94 DKHKQGYICADELRHVMT--TLGERLSEDEVNEMIQEADINGDGRINYEDFVTL 145
K K+ I L H+ G SE EVN +++ +ED+ L
Sbjct: 8 AKRKKKLII---LEHIAKRFEPGREYSEKEVNAILKRF---------HEDYALL 49
>gnl|CDD|184038 PRK13410, PRK13410, molecular chaperone DnaK; Provisional.
Length = 668
Score = 28.4 bits (64), Expect = 1.6
Identities = 12/22 (54%), Positives = 13/22 (59%)
Query: 114 GERLSEDEVNEMIQEADINGDG 135
LSE EVN MIQEA+ D
Sbjct: 499 ASTLSEQEVNRMIQEAEAKADE 520
>gnl|CDD|176730 cd08315, Death_TRAILR_DR4_DR5, Death domain of Tumor necrosis
factor-Related Apoptosis-Inducing Ligand Receptors.
Death Domain (DD) found in Tumor necrosis factor-Related
Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals,
this family includes TRAILR1 (also called DR4 or
TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or
KILLER). They function as receptors for the cytokine
TRAIL and are involved in apoptosis signaling pathways.
TRAIL preferentially induces apoptosis in cancer cells
while exhibiting little toxicity in normal cells. DDs
are protein-protein interaction domains found in a
variety of domain architectures. Their common feature is
that they form homodimers by self-association or
heterodimers by associating with other members of the DD
superfamily including CARD (Caspase activation and
recruitment domain), DED (Death Effector Domain), and
PYRIN. They serve as adaptors in signaling pathways and
can recruit other proteins into signaling complexes.
Length = 96
Score = 27.3 bits (61), Expect = 1.7
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 81 DSTEEIKQAFQVFDKHKQGYICADELRHVMTTLGERLSEDEVNEMIQEADINGD 134
D E ++++F F K + D +M LG LSE+E++ + +
Sbjct: 1 DPQETLRRSFDHFIKE----VPFDSWNRLMRQLG--LSENEIDVAKANERVTRE 48
>gnl|CDD|117542 pfam08976, DUF1880, Domain of unknown function (DUF1880). This
domain is found predominantly in DJ binding protein. It
has no known function.
Length = 122
Score = 27.5 bits (60), Expect = 1.8
Identities = 8/32 (25%), Positives = 19/32 (59%)
Query: 117 LSEDEVNEMIQEADINGDGRINYEDFVTLMTS 148
L++++ + + E +N GR+ Y DF++ +
Sbjct: 4 LTDEQFDRLWNELPVNAKGRLKYPDFLSKFSI 35
>gnl|CDD|240152 cd05025, S-100A1, S-100A1: S-100A1 domain found in proteins similar
to S100A1. S100A1 is a calcium-binding protein belonging
to a large S100 vertebrate-specific protein family
within the EF-hand superfamily of calcium-binding
proteins. Note that the S-100 hierarchy, to which this
S-100A1 group belongs, contains only S-100 EF-hand
domains, other EF-hands have been modeled separately. As
is the case with many other members of S100 protein
family, S100A1 is implicated in intracellular and
extracellular regulatory activities, including
interaction with myosin-associated twitchin kinase,
actin-capping protein CapZ, sinapsin I, and tubulin.
Structural data suggests that S100A1 proteins exist
within cells as antiparallel homodimers, while
heterodimers with S100A4 and S100B also has been
reported. Upon binding calcium S100A1 changes
conformation to expose a hydrophobic cleft which is the
interaction site of S100A1 with its more that 20 known
target proteins.
Length = 92
Score = 26.8 bits (59), Expect = 2.3
Identities = 11/29 (37%), Positives = 23/29 (79%)
Query: 120 DEVNEMIQEADINGDGRINYEDFVTLMTS 148
D V+++++E D NGDG +++++FV L+ +
Sbjct: 52 DAVDKIMKELDENGDGEVDFQEFVVLVAA 80
>gnl|CDD|233996 TIGR02750, TraN_Ftype, type-F conjugative transfer system
mating-pair stabilization protein TraN. TraN is a large
cysteine-rich outer membrane protein involved in the
mating-pair stabilization (adhesin) component of the
F-type conjugative plamid transfer system. TraN is
believed to interact with the core type IV secretion
system apparatus through the TraV protein.
Length = 572
Score = 27.9 bits (62), Expect = 2.4
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 10/51 (19%)
Query: 41 GLTPTEAELLDLIREIDVNQRGTIDFPEFLTVMARKLNTPDSTEEIKQAFQ 91
G+TP E + ++ +IDF F + PD+ EI Q Q
Sbjct: 529 GITPEELQQINF---------ESIDFSPFYEDLHNNQKLPDND-EITQRLQ 569
>gnl|CDD|217077 pfam02514, CobN-Mg_chel, CobN/Magnesium Chelatase. This family
contains a domain common to the cobN protein and to
magnesium protoporphyrin chelatase. CobN is implicated
in the conversion of hydrogenobyrinic acid a,c-diamide
to cobyrinic acid. Magnesium protoporphyrin chelatase is
involved in chlorophyll biosynthesis.
Length = 1079
Score = 27.9 bits (63), Expect = 2.4
Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 21/81 (25%)
Query: 46 EAELLDLIREIDVNQRGTIDFPEFLTVMARKLNTPDSTEEIKQAFQVFDKHKQGYICADE 105
E+L+L E+ +++ DF EFL + L E+K++
Sbjct: 527 REEILELAEELGLDRDLGEDFEEFLERLHDYL------CELKESQ--------------- 565
Query: 106 LRHVMTTLGERLSEDEVNEMI 126
+ + GE +E+ E++
Sbjct: 566 IPDGLHVFGEPPEGEELVELL 586
>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 = 27.9 bits (63), Expect = 2.4
Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 10/49 (20%)
Query: 96 HKQGYICADE-LRHVMTTLGERLSEDEVNEMIQEADINGDG-RINYEDF 142
K+ DE VM + E ++ E++ + DG RI++ED
Sbjct: 367 SKEKVELPDEDKEEVMEAVEEEFADAEIDTI--------DGVRIDFEDG 407
>gnl|CDD|129223 TIGR00117, acnB, aconitate hydratase 2. Aconitate hydratase
(aconitase) is an enzyme of the TCA cycle. This model
describes aconitase 2, AcnB, which has weak similarity
to aconitase 1. It is found almost exclusively in the
Proteobacteria [Energy metabolism, TCA cycle].
Length = 844
Score = 27.6 bits (61), Expect = 2.7
Identities = 15/50 (30%), Positives = 18/50 (36%), Gaps = 3/50 (6%)
Query: 18 SFFNRQGDGR---IPIHELGTVMRFLGLTPTEAELLDLIREIDVNQRGTI 64
+F NR G G + EL V LG PT E + E D
Sbjct: 781 NFPNRMGTGANVYLGSAELAAVCALLGKIPTPEEYQTYVSEKDKTAVDKT 830
>gnl|CDD|240150 cd05023, S-100A11, S-100A11: S-100A11 domain found in proteins
similar to S100A11. S100A11 is a member of the S-100
domain family within EF-hand Ca2+-binding proteins
superfamily. Note that the S-100 hierarchy, to which
this S-100A11 group belongs, contains only S-100
EF-hand domains, other EF-hands have been modeled
separately. S100 proteins exhibit unique patterns of
tissue- and cell type-specific expression and have been
implicated in the Ca2+-dependent regulation of diverse
physiological processes, including cell cycle
regulation, differentiation, growth, and metabolic
control . S100 proteins have also been associated with
a variety of pathological events, including neoplastic
transformation and neurodegenerative diseases such as
Alzheimer's, usually via over expression of the
protein. S100A11 is expressed in smooth muscle and
other tissues and involves in calcium-dependent
membrane aggregation, which is important for cell
vesiculation . As is the case for many other S100
proteins, S100A11 is homodimer, which is able to form a
heterodimer with S100B through subunit exchange. Ca2+
binding to S100A11 results in a conformational change
in the protein, exposing a hydrophobic surface that
interacts with target proteins. In addition to binding
to annexin A1 and A6 S100A11 also interacts with actin
and transglutaminase.
Length = 89
Score = 26.3 bits (58), Expect = 2.8
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 49 LLDLIREIDVNQRGTIDFPEFL 70
L +++++D+N G +DF EFL
Sbjct: 54 LDRMMKKLDLNSDGQLDFQEFL 75
>gnl|CDD|219990 pfam08726, efhand_Ca_insen, Ca2+ insensitive EF hand. EF hands are
helix-loop-helix binding motifs involved in the
regulation of many cellular processes. EF hands usually
bind to Ca2+ ions which causes a major conformational
change that allows the protein to interact with its
designated targets. This domain corresponds to an EF
hand which has partially or entirely lost its
calcium-binding properties. The calcium insensitive EF
hand is still able to mediate protein-protein
recognition.
Length = 69
Score = 26.1 bits (58), Expect = 2.8
Identities = 8/28 (28%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 81 DSTEEIKQAFQVFDKHKQGYICADELRH 108
D+ E+++Q+F+ + K Y+ ++LR
Sbjct: 3 DTAEQVEQSFRALAEGK-PYVTEEDLRR 29
>gnl|CDD|240149 cd05022, S-100A13, S-100A13: S-100A13 domain found in proteins
similar to S100A13. S100A13 is a calcium-binding protein
belonging to a large S100 vertebrate-specific protein
family within the EF-hand superfamily of calcium-binding
proteins. Note that the S-100 hierarchy, to which this
S-100A13 group belongs, contains only S-100 EF-hand
domains, other EF-hands have been modeled separately.
S100A13 is involved in the cellular export of
interleukin-1 (IL-1) and of fibroblast growth factor-1
(FGF-1), which plays an important role in angiogenesis
and tissue regeneration. Export is based on the
CuII-dependent formation of multiprotein complexes
containing the S100A13 protein. Assembly of these
complexes occurs near the inner surface of the plasma
membrane. Binding of two Ca(II) ions per monomer
triggers key conformational changes leading to the
creation of two identical and symmetrical Cu(II)-binding
sites on the surface of the protein, close to the
interface between the two monomers. These Cu(II)-binding
sites are unique among the S100 proteins, which are
reported to bind Cu(II) or Zn(II) ions in addition to
Ca(II) ions. In addition, the three-dimensional
structure of S100A13 differs significantly from those of
other S100 proteins; the hydrophobic pocket that largely
contributes to protein-protein interactions in other
S100 proteins is absent in S100A13. The structure of
S100A13 contains a large patch of negatively charged
residues flanked by dense cationic clusters, formed
mostly from positively charged residues from the
C-terminal end, which plays major role in binding FGF-1.
Length = 89
Score = 26.5 bits (59), Expect = 2.8
Identities = 9/42 (21%), Positives = 23/42 (54%), Gaps = 6/42 (14%)
Query: 105 ELRHVMTTLGERLSEDEVNEMIQEADINGDGRINYEDFVTLM 146
+L H++ + + E ++ D+N D ++++E+F L+
Sbjct: 38 QLPHLLKDVEG------LEEKMKNLDVNQDSKLSFEEFWELI 73
>gnl|CDD|222253 pfam13597, NRDD, Anaerobic ribonucleoside-triphosphate reductase.
Length = 542
Score = 27.5 bits (62), Expect = 3.2
Identities = 14/38 (36%), Positives = 15/38 (39%), Gaps = 5/38 (13%)
Query: 59 NQRGTIDFPEFLTVMA---RKLNTPDSTEEIKQAFQVF 93
G F F T +A RK EEIKQ Q F
Sbjct: 100 EFAGAQAFSSFDTYLAPFVRKDY--LDYEEIKQHLQEF 135
>gnl|CDD|233830 TIGR02350, prok_dnaK, chaperone protein DnaK. Members of this
family are the chaperone DnaK, of the DnaK-DnaJ-GrpE
chaperone system. All members of the seed alignment were
taken from completely sequenced bacterial or archaeal
genomes and (except for Mycoplasma sequence) found
clustered with other genes of this systems. This model
excludes DnaK homologs that are not DnaK itself, such as
the heat shock cognate protein HscA (TIGR01991).
However, it is not designed to distinguish among DnaK
paralogs in eukaryotes. Note that a number of dnaK genes
have shadow ORFs in the same reverse (relative to dnaK)
reading frame, a few of which have been assigned
glutamate dehydrogenase activity. The significance of
this observation is unclear; lengths of such shadow ORFs
are highly variable as if the presumptive protein
product is not conserved [Protein fate, Protein folding
and stabilization].
Length = 595
Score = 27.3 bits (61), Expect = 3.2
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 117 LSEDEVNEMIQEADIN 132
LSE+E+ M++EA+ N
Sbjct: 498 LSEEEIERMVKEAEAN 513
>gnl|CDD|220526 pfam10025, DUF2267, Uncharacterized conserved protein (DUF2267).
This domain, found in various hypothetical bacterial
proteins, has no known function.
Length = 126
Score = 26.4 bits (59), Expect = 3.7
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 17/61 (27%)
Query: 65 DFPEFLTVMARKLNTPDSTEEIKQAFQVFDKHKQGYICADELRHVMTTLGERLSEDEVNE 124
D+ EFL + + PD ++A++ R V+ TL +RL+ +E +
Sbjct: 1 DYDEFLEDVRERAGLPD----REEAYRA-------------TRAVLRTLRDRLTGEEAAD 43
Query: 125 M 125
+
Sbjct: 44 L 44
>gnl|CDD|201938 pfam01726, LexA_DNA_bind, LexA DNA binding domain. This is the DNA
binding domain of the LexA SOS regulon repressor which
prevents expression of DNA repair proteins. The aligned
region contains a variant form of the helix-turn-helix
DNA binding motif. This domain is found associated with
pfam00717 the auto-proteolytic domain of LexA
EC:3.4.21.88.
Length = 63
Score = 25.4 bits (56), Expect = 3.8
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 11/63 (17%)
Query: 41 GLTPTEAELLDLIREIDVNQRGTIDFPEFLTVMARKLN--TPDSTEEIKQAFQVFDKHKQ 98
LT + E+LD I+ + + G +P +AR L +P++ EE +A + ++
Sbjct: 1 PLTERQREVLDFIKA-SIEETG---YPPSRREIARALGLRSPNAAEEHLKALE-----RK 51
Query: 99 GYI 101
GYI
Sbjct: 52 GYI 54
>gnl|CDD|168322 PRK05973, PRK05973, replicative DNA helicase; Provisional.
Length = 237
Score = 26.9 bits (60), Expect = 4.1
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 39 FLGLTPTEAELLDLIREIDVNQRGTIDFPEFLT 71
F L TE ++ D +R + ++ D EF T
Sbjct: 97 FFTLEYTEQDVRDRLRALGADRAQFADLFEFDT 129
>gnl|CDD|234663 PRK00142, PRK00142, putative rhodanese-related sulfurtransferase;
Provisional.
Length = 314
Score = 26.7 bits (60), Expect = 4.3
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 114 GERLSEDEVNEMIQEAD-INGDGRINYE 140
G L EVNE++ + D + D R +YE
Sbjct: 111 GTYLKPKEVNELLDDPDVVFIDMRNDYE 138
>gnl|CDD|201211 pfam00404, Dockerin_1, Dockerin type I repeat. The dockerin repeat
is the binding partner of the cohesin domain pfam00963.
The cohesin-dockerin interaction is the crucial
interaction for complex formation in the cellulosome.
The dockerin repeats, each bearing homology to the
EF-hand calcium-binding loop bind calcium.
Length = 21
Score = 24.1 bits (54), Expect = 4.7
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 130 DINGDGRINYEDFVTL 145
D+NGDG++N D L
Sbjct: 1 DVNGDGKVNALDLALL 16
>gnl|CDD|202285 pfam02563, Poly_export, Polysaccharide biosynthesis/export
protein. This is a family of periplasmic proteins
involved in polysaccharide biosynthesis and/or export.
Length = 83
Score = 25.6 bits (57), Expect = 4.8
Identities = 11/41 (26%), Positives = 15/41 (36%)
Query: 51 DLIREIDVNQRGTIDFPEFLTVMARKLNTPDSTEEIKQAFQ 91
+L E+ V+ GTI P V L + E I
Sbjct: 29 ELSGEVRVDPDGTISLPLVGPVKVAGLTPEELEELIADKLA 69
>gnl|CDD|214360 CHL00094, dnaK, heat shock protein 70.
Length = 621
Score = 26.6 bits (59), Expect = 5.3
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 117 LSEDEVNEMIQEADINGD 134
L +DEV M++EA+ N
Sbjct: 502 LPKDEVERMVKEAEKNAA 519
>gnl|CDD|240154 cd05027, S-100B, S-100B: S-100B domain found in proteins similar to
S100B. S100B is a calcium-binding protein belonging to a
large S100 vertebrate-specific protein family within the
EF-hand superfamily of calcium-binding proteins. Note
that the S-100 hierarchy, to which this S-100B group
belongs, contains only S-100 EF-hand domains, other
EF-hands have been modeled separately. S100B is most
abundant in glial cells of the central nervous system,
predominately in astrocytes. S100B is involved in signal
transduction via the inhibition of protein
phoshorylation, regulation of enzyme activity and by
affecting the calcium homeostasis. Upon calcium binding
the S100B homodimer changes conformation to expose a
hydrophobic cleft, which represents the interaction site
of S100B with its more than 20 known target proteins.
These target proteins include several cellular
architecture proteins such as tubulin and GFAP; S100B
can inhibit polymerization of these oligomeric
molecules. Furthermore, S100B inhibits the
phosphorylation of multiple kinase substrates including
the Alzheimer protein tau and neuromodulin (GAP-43)
through a calcium-sensitive interaction with the protein
substrates.
Length = 88
Score = 25.6 bits (56), Expect = 6.0
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 94 DKHKQGYICADEL-RHVMTTLGERLSEDEVNEMIQEA-DINGDGRINYEDFVTLMT 147
DKHK EL + ++ E + E EV + + E D +GDG ++++F+ +
Sbjct: 23 DKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMAFVA 78
>gnl|CDD|112487 pfam03672, UPF0154, Uncharacterized protein family (UPF0154). This
family contains a set of short bacterial proteins of
unknown function.
Length = 64
Score = 24.8 bits (54), Expect = 6.6
Identities = 7/29 (24%), Positives = 17/29 (58%)
Query: 101 ICADELRHVMTTLGERLSEDEVNEMIQEA 129
I D +R + +G + SE ++N++++
Sbjct: 32 INEDMIRMMYMQMGRKPSEKQINQIMRAI 60
>gnl|CDD|182629 PRK10665, PRK10665, nitrogen regulatory protein P-II 2;
Provisional.
Length = 112
Score = 25.7 bits (56), Expect = 6.7
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 1 MADQLTEEQINDFKEAFSFFNRQGDGRIPIHELGTVMR 38
+AD +E I+ +A ++ + GDG+I + EL V+R
Sbjct: 65 IADDQLDEVIDIISKA-AYTGKIGDGKIFVAELQRVIR 101
>gnl|CDD|234715 PRK00290, dnaK, molecular chaperone DnaK; Provisional.
Length = 627
Score = 26.6 bits (60), Expect = 6.9
Identities = 6/16 (37%), Positives = 13/16 (81%)
Query: 117 LSEDEVNEMIQEADIN 132
LS++E+ M+++A+ N
Sbjct: 500 LSDEEIERMVKDAEAN 515
>gnl|CDD|215053 PLN00094, PLN00094, aconitate hydratase 2; Provisional.
Length = 938
Score = 26.4 bits (58), Expect = 6.9
Identities = 21/81 (25%), Positives = 32/81 (39%), Gaps = 10/81 (12%)
Query: 18 SFFNRQGDGR---IPIHELGTVMRFLGLTPTEAELLDLIREIDVNQRGTIDF------PE 68
+F NR G G + EL V LG PT E L + ++D T + PE
Sbjct: 855 NFPNRLGKGANVYLASAELAAVAAILGRLPTVEEYLSYMEKLDATASDTYRYLNFDELPE 914
Query: 69 FLTVMARKLNTPDSTEEIKQA 89
++ A K+ + E +
Sbjct: 915 YVES-AEKVEISEEMREAAKK 934
>gnl|CDD|130699 TIGR01638, Atha_cystat_rel, Arabidopsis thaliana cystatin-related
protein. This model represents a family similar in
sequence and probably homologous to a large family of
cysteine proteinase inhibitors, or cystatins, as
described by Pfam model pfam00031. Cystatins may help
plants resist attack by insects.
Length = 92
Score = 25.2 bits (55), Expect = 7.5
Identities = 12/48 (25%), Positives = 18/48 (37%), Gaps = 2/48 (4%)
Query: 42 LTPTEAELLDLIREIDVNQRGTIDFPEFLTVMARKLNTPDSTEEIKQA 89
T+ L+L+ + N RG ++T AR PD Q
Sbjct: 26 YNDTKFLNLELVEVVRANYRGGAKSKSYITFEARD--KPDGPLGEYQQ 71
>gnl|CDD|221649 pfam12580, TPPII, Tripeptidyl peptidase II. This domain family is
found in bacteria and eukaryotes, and is approximately
190 amino acids in length. The family is found in
association with pfam00082. Tripeptidyl peptidase II
(TPPII) is a crucial component of the proteolytic
cascade acting downstream of the 26S proteasome in the
ubiquitin-proteasome pathway. It is an amino peptidase
belonging to the subtilase family removing tripeptides
from the free N terminus of oligopeptides.
Length = 188
Score = 26.1 bits (58), Expect = 7.7
Identities = 23/114 (20%), Positives = 39/114 (34%), Gaps = 41/114 (35%)
Query: 42 LTPTEAELLDLIREIDV--NQRGTIDFPEFLTVMARKLNTPDSTE-------------EI 86
L PTEA++ L DV + R + V+ N + E E
Sbjct: 20 LRPTEAKIKPLGAPRDVLPSGRQI-----YALVLTYNFNLAKAAEVTPRLPLLSDLLYES 74
Query: 87 K---QAFQVFDKHKQGYICAD------------------ELRHVMTTLGERLSE 119
+ Q + +FD +K+ D ++RH +L E+L +
Sbjct: 75 EFESQLWMIFDANKRLVGSGDAYPHRSTKLEKGDYTLRLQIRHEDRSLLEKLKD 128
>gnl|CDD|182066 PRK09765, PRK09765, PTS system 2-O-a-mannosyl-D-glycerate specific
transporter subunit IIABC; Provisional.
Length = 631
Score = 26.2 bits (58), Expect = 7.7
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 108 HVMTTLGERLSEDEVNEMIQEAD 130
++T L RL++DE+ IQ A
Sbjct: 117 QLLTALTTRLADDEIRARIQSAT 139
>gnl|CDD|226571 COG4086, COG4086, Predicted secreted protein [Function unknown].
Length = 299
Score = 25.9 bits (57), Expect = 8.2
Identities = 9/26 (34%), Positives = 17/26 (65%)
Query: 109 VMTTLGERLSEDEVNEMIQEADINGD 134
+ TLGE LSE + ++++E ++ D
Sbjct: 37 PIVTLGEDLSETQKQQLLKEMGVDPD 62
>gnl|CDD|216059 pfam00685, Sulfotransfer_1, Sulfotransferase domain.
Length = 254
Score = 25.8 bits (57), Expect = 8.9
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 29 PIHELGTVMRFLGLTPTEAELLDLIR 54
P E+ + FLG+ TE EL +++
Sbjct: 170 PRGEIKKIAEFLGIPLTEEELDKIVK 195
>gnl|CDD|235616 PRK05813, PRK05813, single-stranded DNA-binding protein;
Provisional.
Length = 219
Score = 25.8 bits (57), Expect = 9.0
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 3/33 (9%)
Query: 70 LTVMARKLNTPDSTEEIKQAFQVFDKHKQGYIC 102
LTV AR + D +IK ++F GYIC
Sbjct: 90 LTVFARNIEYCDERSDIKNPNEIF---LDGYIC 119
>gnl|CDD|216544 pfam01514, YscJ_FliF, Secretory protein of YscJ/FliF family. This
family includes proteins that are related to the YscJ
lipoprotein, and the amino terminus of FliF, the
flageller M-ring protein. The members of the YscJ family
are thought to be involved in secretion of several
proteins. The FliF protein ring is thought to be part of
the export apparatus for flageller proteins, based on
the similarity to YscJ proteins.
Length = 206
Score = 25.7 bits (57), Expect = 9.0
Identities = 10/31 (32%), Positives = 13/31 (41%), Gaps = 3/31 (9%)
Query: 110 MTTLGERLSEDEVNEMIQEADINGDGRINYE 140
TL LSE + NE++ G I E
Sbjct: 27 YVTLYTGLSEKDANEVLAALLQAG---IPAE 54
>gnl|CDD|183903 PRK13230, PRK13230, nitrogenase reductase-like protein; Reviewed.
Length = 279
Score = 25.9 bits (57), Expect = 9.1
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 59 NQRGTIDFPEFLTVMARKLNT 79
N R ID P+ + A+K+ T
Sbjct: 183 NGRSVIDAPDIVEEFAKKIGT 203
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
0.319 0.137 0.386
Gapped
Lambda K H
0.267 0.0708 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,967,297
Number of extensions: 746969
Number of successful extensions: 1165
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1148
Number of HSP's successfully gapped: 130
Length of query: 148
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 60
Effective length of database: 7,034,450
Effective search space: 422067000
Effective search space used: 422067000
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 (21.7 bits)
S2: 54 (24.6 bits)