RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13382
(237 letters)
>gnl|CDD|146145 pfam03357, Snf7, Snf7. This family of proteins are involved in
protein sorting and transport from the endosome to the
vacuole/lysosome in eukaryotic cells. Vacuoles/lysosomes
play an important role in the degradation of both lipids
and cellular proteins. In order to perform this
degradative function, vacuoles/lysosomes contain
numerous hydrolases which have been transported in the
form of inactive precursors via the biosynthetic pathway
and are proteolytically activated upon delivery to the
vacuole/lysosome. The delivery of transmembrane
proteins, such as activated cell surface receptors to
the lumen of the vacuole/lysosome, either for
degradation/downregulation, or in the case of
hydrolases, for proper localisation, requires the
formation of multivesicular bodies (MVBs). These late
endosomal structures are formed by invaginating and
budding of the limiting membrane into the lumen of the
compartment. During this process, a subset of the
endosomal membrane proteins is sorted into the forming
vesicles. Mature MVBs fuse with the vacuole/lysosome,
thereby releasing cargo containing vesicles into its
hydrolytic lumen for degradation. Endosomal proteins
that are not sorted into the intralumenal MVB vesicles
are either recycled back to the plasma membrane or Golgi
complex, or remain in the limiting membrane of the MVB
and are thereby transported to the limiting membrane of
the vacuole/lysosome as a consequence of fusion.
Therefore, the MVB sorting pathway plays a critical role
in the decision between recycling and degradation of
membrane proteins. A few archaeal sequences are also
present within this family.
Length = 169
Score = 138 bits (350), Expect = 2e-41
Identities = 58/167 (34%), Positives = 103/167 (61%), Gaps = 2/167 (1%)
Query: 17 KNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMESVKIMAKDLVRTRKYAKKF 76
+ +L KA+R+LD++++ +E++ KKL A+IKK+AK+G ++ I+ K R K +
Sbjct: 1 EAILSLRKAIRELDKKQESLEKKIKKLEAEIKKLAKKGNKDAALILLKQKKRYEKQLDQL 60
Query: 77 MMMKANIQAVSLKIQTLRSQNAMAEAMKGCSRAMQNMNRQMNLPQIQRILQEFEKQSEIM 136
AN++ V + I+ ++ + AMKG ++AM+ MN+ M++ +I ++ E E Q E
Sbjct: 61 DGQLANLEQVRMAIENAKTNQEVLNAMKGGAKAMKAMNKNMDIDKIDDLMDEIEDQMEKA 120
Query: 137 DMKEEMMNDAMDDAMDADEDEDETNAVVTQVLDELGLQLGDQLASIP 183
D EM++D +DDA +EDE+E +A + +LDE+G + +L S P
Sbjct: 121 DEISEMLSDTLDDA--DEEDEEELDAELDALLDEIGDEELVELPSAP 165
>gnl|CDD|227778 COG5491, VPS24, Conserved protein implicated in secretion [Cell
motility and secretion].
Length = 204
Score = 66.0 bits (161), Expect = 3e-13
Identities = 47/165 (28%), Positives = 79/165 (47%), Gaps = 8/165 (4%)
Query: 37 EQQEKKLIADIKKMAKEGQMESVKIMAKDLVRTRKYAK--KFMMMKANIQAVSLKIQTLR 94
E+Q KKL+ ++K+ AK+GQ+ +I K R R + K ++ + A ++Q+L
Sbjct: 6 ERQAKKLVRELKQEAKKGQVLLNEIAKKAPNRRRLAEELYKLRKARSRLDASISRLQSLD 65
Query: 95 SQNAMAEAMKGCSRAMQNMNRQMN-LPQIQRILQEFEKQSEIMD---MKEEMMNDAMDDA 150
+ M+ S M MN L I+RI+Q FE Q ++ ++ E M++ MD
Sbjct: 66 TMLFEKVVMRQVSGDMAKAAMYMNELESIRRIMQLFETQFLALELVQLRLETMDELMDVV 125
Query: 151 MDADEDEDETNA--VVTQVLDELGLQLGDQLASIPDPASSMMSDK 193
+ ED +V +VL E+GL+L + S+P S
Sbjct: 126 VGDPVLEDLEELDELVNKVLPEIGLELDESEQSLPANVVENGSVP 170
>gnl|CDD|240422 PTZ00446, PTZ00446, vacuolar sorting protein SNF7-like;
Provisional.
Length = 191
Score = 33.5 bits (76), Expect = 0.044
Identities = 22/147 (14%), Positives = 74/147 (50%)
Query: 24 KAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMESVKIMAKDLVRTRKYAKKFMMMKANI 83
+A+ L++++ +E++ K+L + K+ ++ QM + KI+ K + + + + +
Sbjct: 34 EAIDALEKKQVQVEKKIKQLEIEAKQKVEQNQMSNAKILLKRKKLYEQEIENILNNRLTL 93
Query: 84 QAVSLKIQTLRSQNAMAEAMKGCSRAMQNMNRQMNLPQIQRILQEFEKQSEIMDMKEEMM 143
+ + ++ + A+ + + +N ++N ++++I+ ++ +I + + +
Sbjct: 94 EDNMINLENMHLHKIAVNALSYAANTHKKLNNEINTQKVEKIIDTIQENKDIQEEINQAL 153
Query: 144 NDAMDDAMDADEDEDETNAVVTQVLDE 170
+ + + +D DE + E + + Q ++E
Sbjct: 154 SFNLLNNVDDDEIDKELDLLKEQTMEE 180
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 33.3 bits (76), Expect = 0.12
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 1/69 (1%)
Query: 7 RKITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMESVKIMAKDL 66
+K TP+ + K+ AL K + LD+E E+ +KL + G + V A
Sbjct: 1146 KKTTPKSLWLKDLDALEKELDKLDKEDAKAEEAREKLQRA-AARGESGAAKKVSRQAPKK 1204
Query: 67 VRTRKYAKK 75
+K KK
Sbjct: 1205 PAPKKTTKK 1213
>gnl|CDD|235152 PRK03705, PRK03705, glycogen debranching enzyme; Provisional.
Length = 658
Score = 32.3 bits (74), Expect = 0.19
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 4/28 (14%)
Query: 203 GSGSNHSNNHGGGGGSTLSDADADLQAR 230
G+ +N+SNNHG G AD DL R
Sbjct: 468 GTNNNYSNNHGKEG----LGADLDLVER 491
>gnl|CDD|221784 pfam12810, Gly_rich, Glycine rich protein. This family of proteins
is greatly expanded in Trichomonas vaginalis. The
proteins are composed of several glycine rich motifs
interspersed through the sequence. Although many
proteins have been annotated by similarity in the family
these annotations given the biased composition of the
sequences these are unlikely to be functionally
relevant.
Length = 248
Score = 31.8 bits (73), Expect = 0.21
Identities = 9/21 (42%), Positives = 14/21 (66%), Gaps = 3/21 (14%)
Query: 202 GGSGSNHSNNH---GGGGGST 219
GG G N ++++ G GGG+T
Sbjct: 75 GGDGGNDNSSNDGSGSGGGAT 95
>gnl|CDD|240425 PTZ00464, PTZ00464, SNF-7-like protein; Provisional.
Length = 211
Score = 31.7 bits (72), Expect = 0.22
Identities = 38/208 (18%), Positives = 80/208 (38%), Gaps = 12/208 (5%)
Query: 1 MEWLFGR-KITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMESV 59
M LFG+ TP+ L + + +D ++ + KL I++ Q
Sbjct: 1 MNRLFGKKNKTPKPTLEDASKRIGGRSEVVDARINKIDAELMKLKEQIQRTRGMTQSRHK 60
Query: 60 KIMAKDLVRTRKYAKKFMMMKA---NIQAVSLKIQTLRSQNAMAEAMKGCSRAMQNMNRQ 116
+ + L + R Y + MM N+ + ++++ +AMK ++ ++ ++
Sbjct: 61 QRAMQLLQQKRMYQNQQDMMMQQQFNMDQLQFTTESVKDTKVQVDAMKQAAKTLKKQFKK 120
Query: 117 MNLPQIQRILQEFEKQSEIMDMKEEMMNDAMDDAMDADEDEDETNAVVTQVLDELGLQLG 176
+N+ +++ + E E +E+M A D D DEDE LD L +
Sbjct: 121 LNVDKVEDLQDELADLYEDTQEIQEIMGRAYDVPDDIDEDEMLGE------LDALDFDME 174
Query: 177 DQLASIPDPASSMMSDKGKTPVAIPGGS 204
+ + + ++ G +P
Sbjct: 175 KEADA--SYLADALAVPGTKLPDVPTDE 200
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 31.6 bits (72), Expect = 0.42
Identities = 20/182 (10%), Positives = 59/182 (32%), Gaps = 2/182 (1%)
Query: 7 RKITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMESVKIMAKDL 66
+ TP++M ++ +A+ + + ++ +E++L + K A + + +K K
Sbjct: 1122 KNTTPKDMWLEDLDKFEEALEEQEEVEEKEIAKEQRLKSKTKGKASKLRKPKLKKKEKKK 1181
Query: 67 VRTRKYAKKFMMMKANIQAVSLKIQTLRSQNAMAEAMKGCSRAMQNMNRQMNLPQIQRIL 126
++ K + N + V + + ++ Q P+ +
Sbjct: 1182 KKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKKSNSSGSDQEDDEEQKTKPKKSSVK 1241
Query: 127 QEFEKQSEIMDMKEEMMNDAMDDAMDADEDEDETNAVVTQVLDELGLQLGDQLASIPDPA 186
+ K++ E+ + DD + ++ + + +
Sbjct: 1242 RLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPK--RVSAVQYSPPPPSKRPDGESNGG 1299
Query: 187 SS 188
S
Sbjct: 1300 SK 1301
>gnl|CDD|213889 TIGR04059, Ald_deCOase, long-chain fatty aldehyde decarbonylase.
This cyanobacterial family of fatty aldehyde
decarbonylases acts on mainly C16 and C18 substrates to
form hydrocarbons and carbon monoxide. Note that the
corresponding EC number (4.1.99.5) dating from 1989
refers to a nonorthologous Pisum sativum enzyme that
acts on C18 and longer chains and attaches the overly
narrow narrow name octadecanal decarbonylase [Central
intermediary metabolism, Other].
Length = 220
Score = 30.5 bits (69), Expect = 0.51
Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 106 CSRAMQNMNRQMNLPQIQRILQEFEKQSEIMDM-KEEMMNDAM 147
++ NR+ NLP + R+L + + ++ M KE ++ D M
Sbjct: 153 VKEELEEANRE-NLPLVWRMLNQVADDAAVLGMEKEALVEDFM 194
>gnl|CDD|173939 cd08180, PDD, 1,3-propanediol dehydrogenase (PPD) catalyzes the
reduction of 3-hydroxypropionaldehyde (3-HPA) to
1,3-propanediol in glycerol metabolism. 1,3-propanediol
dehydrogenase (PPD) plays a role in glycerol metabolism
of some bacteria in anaerobic conditions. In this
degradation pathway, glycerol is converted in a two-step
process to 1,3-propanediol (1,3-PD) which is then
excreted into the extracellular medium. The first
reaction involves the transformation of glycerol into
3-hydroxypropionaldehyde (3-HPA) by a coenzyme
B-12-dependent dehydratase. The second reaction involves
the dismutation of the 3-hydroxypropionaldehyde (3-HPA)
to 1,3-propanediol by the NADH-linked 1,3-propanediol
dehydrogenase (PPD). The enzyme require iron ion for its
function. Because many genes in this pathway are
present in the pdu (propanediol utilisation) operon,
they are also named pdu genes. PPD is a member of the
iron-containing alcohol dehydrogenase superfamily. The
PPD structure has a dehydroquinate synthase-like fold.
Length = 332
Score = 31.0 bits (71), Expect = 0.54
Identities = 11/44 (25%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 108 RAMQNMNRQMNLPQIQRILQEF-EKQSEIMDMKEEMMNDAMDDA 150
A++ + +++N+P+ L+E + E +EM +A+ DA
Sbjct: 273 EAIKQLKKKLNIPE---TLKELGVDKEEFEAAIDEMAENALKDA 313
>gnl|CDD|216284 pfam01074, Glyco_hydro_38, Glycosyl hydrolases family 38
N-terminal domain. Glycosyl hydrolases are key enzymes
of carbohydrate metabolism.
Length = 269
Score = 30.7 bits (70), Expect = 0.59
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 16/69 (23%)
Query: 1 MEWLFGRKITPEEMLRKNQRALNKAMRDLDREK------------QHMEQQEKKLIADIK 48
+ WL+ T +E RK QR + ++ LDR + + + +L IK
Sbjct: 12 VGWLW----TVDETRRKVQRTFSNVLKLLDRYPEFRFIQSEAQFYEWWWEDQPELFKKIK 67
Query: 49 KMAKEGQME 57
K+ EG++E
Sbjct: 68 KLVAEGRLE 76
>gnl|CDD|151707 pfam11266, DUF3066, Protein of unknown function (DUF3066). This
family of proteins with unknown function appears to be
restricted to Cyanobacteria.
Length = 219
Score = 30.5 bits (69), Expect = 0.63
Identities = 11/43 (25%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 106 CSRAMQNMNRQMNLPQIQRILQEFEKQSEIMDM-KEEMMNDAM 147
++ NR+ NLP + ++L + + ++ M KE ++ D M
Sbjct: 152 SKEELEEANRE-NLPLVWKMLNQVADDAAVLGMDKEALVEDFM 193
>gnl|CDD|237879 PRK14983, PRK14983, aldehyde decarbonylase; Provisional.
Length = 231
Score = 30.0 bits (68), Expect = 0.78
Identities = 10/35 (28%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 114 NRQMNLPQIQRILQEFEKQSEIMDM-KEEMMNDAM 147
N++ NLP + ++L + + ++ M KE ++ D M
Sbjct: 170 NKE-NLPLVWKMLNQVADDAAVLGMEKEALVEDFM 203
>gnl|CDD|226659 COG4196, COG4196, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 808
Score = 30.3 bits (68), Expect = 0.94
Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 14/75 (18%)
Query: 148 DDAMDADE---------DEDETNAVVTQVLDELGLQLGDQLASIPDPASSMMSDKGKTPV 198
+DA+ ADE D++ V+ + D LGL + + DP + ++ V
Sbjct: 125 NDALLADEWGAPPVDPVDDEAAYKVLAGIADGLGLPISQVRPAYEDPLERLAAE-----V 179
Query: 199 AIPGGSGSNHSNNHG 213
+P G + S++ G
Sbjct: 180 RLPAGDPVDPSDDRG 194
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 29.5 bits (67), Expect = 1.5
Identities = 14/84 (16%), Positives = 45/84 (53%), Gaps = 4/84 (4%)
Query: 18 NQRALNKAMRDLDREKQHMEQQEKKLIADIKKM--AKEGQMESVKI-MAKDLVRTRKYAK 74
+ L + +++L+ E + +E++ +K+ +KK+ GQ+ K + L+ T++
Sbjct: 328 DFPELKEELKELEEELKELEEELEKIKKLLKKLPKKARGQLPPEKREQLEKLLETKEKLS 387
Query: 75 KFM-MMKANIQAVSLKIQTLRSQN 97
+ + ++ ++ + ++++L S+
Sbjct: 388 EELEELEEELKELKEELESLYSEG 411
>gnl|CDD|200948 pfam00038, Filament, Intermediate filament protein.
Length = 312
Score = 29.1 bits (66), Expect = 1.7
Identities = 25/131 (19%), Positives = 53/131 (40%), Gaps = 29/131 (22%)
Query: 22 LNKAMRDL--------DREKQHMEQQEKKLIADIKKMAKEG--QMESVKIMAKDLVRTRK 71
L KA+ ++ ++ +Q E+ K + ++++ A + S K +L R
Sbjct: 167 LTKALAEIRAQYEELAEKNRQEAEEWYKSKLEELQQAAARNGDALRSAKEEITELRRQ-- 224
Query: 72 YAKKFMMMKANIQAVSLKIQTLRSQNAMAEAMKGCSRAMQNMNRQMNLPQIQRILQEFEK 131
IQ++ +++Q+L+ Q A E + + ++ Q + E E
Sbjct: 225 -----------IQSLEIELQSLKKQKASLERQ--LAELEERYELELA--DYQDTISELE- 268
Query: 132 QSEIMDMKEEM 142
E+ +K EM
Sbjct: 269 -EELQQLKAEM 278
>gnl|CDD|220964 pfam11068, DUF2869, Protein of unknown function (DUF2869). This
bacterial family of proteins has no known function.
Length = 131
Score = 28.3 bits (64), Expect = 1.9
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 16 RKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQ 55
+ Q L + + L++E Q +E Q +K I +I+K + +
Sbjct: 19 EELQAELQEQLTQLEQELQQLEFQGQKAIKEIRKQSAQQI 58
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 29.4 bits (67), Expect = 2.0
Identities = 10/45 (22%), Positives = 28/45 (62%), Gaps = 3/45 (6%)
Query: 12 EEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIA---DIKKMAKE 53
E+ L + + L++ + L++ ++ +E++EK+L +++K +E
Sbjct: 88 EKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEE 132
>gnl|CDD|217902 pfam04111, APG6, Autophagy protein Apg6. In yeast, 15 Apg proteins
coordinate the formation of autophagosomes. Autophagy is
a bulk degradation process induced by starvation in
eukaryotic cells. Apg6/Vps30p has two distinct functions
in the autophagic process, either associated with the
membrane or in a retrieval step of the carboxypeptidase
Y sorting pathway.
Length = 356
Score = 29.1 bits (65), Expect = 2.1
Identities = 12/59 (20%), Positives = 27/59 (45%), Gaps = 5/59 (8%)
Query: 7 RKITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIAD-----IKKMAKEGQMESVK 60
R + E L K L+ + +L EK+ +E +E + + + + E ++S++
Sbjct: 81 RLLDELEELEKEDDDLDGELVELQEEKEQLENEELQYLREYNLFDRNNLQLEDNLQSLE 139
>gnl|CDD|233207 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP)
Family protein. [Transport and binding proteins,
Other].
Length = 617
Score = 29.2 bits (66), Expect = 2.1
Identities = 31/165 (18%), Positives = 58/165 (35%), Gaps = 30/165 (18%)
Query: 15 LRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMESVKIMAKDLVRTRKYAK 74
R Q K + R E+ K L+ ++ +AK G++ + +M A
Sbjct: 12 GRVAQDGSWKQLVSRLRGCFCRERPRKHLLKNVSGVAKPGEL--LAVMGS------SGAG 63
Query: 75 KFMMMK--ANIQAVSLKIQTLRSQNAMAEAMKGCSRAMQNMNRQMNLPQIQRI---LQEF 129
K +M A +K N M ++ +++ I +Q+
Sbjct: 64 KTTLMNALAFRSPKGVKGSGSVLLNGMP----------------IDAKEMRAISAYVQQD 107
Query: 130 EKQSEIMDMKEEMMNDAMDDAMDADEDEDETNAVVTQVLDELGLQ 174
+ + ++E +M A M + E V +VL LGL+
Sbjct: 108 DLFIPTLTVREHLMFQAHL-RMPRRVTKKEKRERVDEVLQALGLR 151
>gnl|CDD|114701 pfam05993, Reovirus_M2, Reovirus major virion structural protein
Mu-1/Mu-1C (M2). This family consists of several
Reovirus major virion structural protein Mu-1/Mu-1C (M2)
sequences. This family is family is thought to play a
role in host cell membrane penetration.
Length = 648
Score = 29.0 bits (64), Expect = 2.7
Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 4/75 (5%)
Query: 6 GRKITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMESVKIMAKD 65
G P R++ A++ L + + ++ L DI M+S+ A D
Sbjct: 121 GPVFIPTRQTMNLDRSIAAALKALAKWEIDLDTAMTLLPPDIPAGEASCNMKSLLAFADD 180
Query: 66 LVR----TRKYAKKF 76
++ +Y K+
Sbjct: 181 ILPDDNLCLRYPKEA 195
>gnl|CDD|189895 pfam01221, Dynein_light, Dynein light chain type 1.
Length = 86
Score = 26.8 bits (60), Expect = 3.2
Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 136 MDMKEEMMNDAMD---DAMDADEDEDETNAVVTQVLDE 170
DM EEM DA++ +A++ E + A + + D+
Sbjct: 8 ADMPEEMQEDAIECAAEALEKFNVEKDIAAHIKKEFDK 45
>gnl|CDD|220506 pfam09989, DUF2229, CoA enzyme activase uncharacterized domain
(DUF2229). Members of this family include various
bacterial hypothetical proteins, as well as CoA enzyme
activases. The exact function of this domain has not, as
yet, been defined.
Length = 218
Score = 28.3 bits (64), Expect = 3.4
Identities = 11/54 (20%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 1 MEWLFGRKITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEG 54
E I+ EE+ ++A+ KA+ + + K+ + ++ ++ +A +++ K+G
Sbjct: 133 YELGKKLGISKEEI----KKAVEKALEEQEAFKKDLRKKGEEALAYLEEEGKKG 182
>gnl|CDD|218115 pfam04502, DUF572, Family of unknown function (DUF572). Family of
eukaryotic proteins with undetermined function.
Length = 321
Score = 28.2 bits (63), Expect = 3.6
Identities = 18/100 (18%), Positives = 32/100 (32%), Gaps = 9/100 (9%)
Query: 12 EEMLRKNQR----ALNKAMRDL-DREKQHMEQQEKKLIADIKKMAKEGQMESVKIMAKDL 66
EE+ R +N + L REK+ E++E++ A IK ++ + E + A D
Sbjct: 155 EELKELQSRRADVDVNSMLEALFRREKKEEEEEEEEDEALIKSLSFGPETEEDRRRADDE 214
Query: 67 VRTRKYAKKFMMMKANIQAVSL----KIQTLRSQNAMAEA 102
+ S I +
Sbjct: 215 DSEDDEEDNDNTPSPKSGSSSPAKPTSILKKSAAKRSEAP 254
>gnl|CDD|220767 pfam10459, Peptidase_S46, Peptidase S46. Dipeptidyl-peptidase 7
(DPP-7) is the best characterized member of this family.
It is a serine peptidase that is located on the cell
surface and is predicted to have two N-terminal
transmembrane domains.
Length = 696
Score = 28.3 bits (64), Expect = 3.6
Identities = 27/163 (16%), Positives = 56/163 (34%), Gaps = 24/163 (14%)
Query: 17 KNQRALNKAMRDLD-REKQHMEQQEKKLIADIKKMAKEGQMESVKIMAKDLVRTRKYAKK 75
KN + + ++DLD ++ + +E L A +KK G KY
Sbjct: 309 KNSIGMLEGLKDLDLLARK--QAREAALRAWVKKDPARG---------------AKYGDA 351
Query: 76 FMMMKANIQAVSLKIQTLRSQNAMAEAMKGCSRAMQNMNRQMNLPQIQRILQEFEKQSEI 135
+ A+ + + L + E + R + +R + E++
Sbjct: 352 L----DELAALYAERRELARRYFYLEEAFRSGELLS-AARTLVRLAKEREKPDAEREPGY 406
Query: 136 MDMKEEMMNDAMDDAMDADEDEDETNAVVTQVLDELGLQLGDQ 178
+ + ++ +D D + AV+ +L+E LG
Sbjct: 407 QERDLPRLEQQLER-IDKPYDAEVDKAVLAAMLEEYRELLGAD 448
>gnl|CDD|227952 COG5665, NOT5, CCR4-NOT transcriptional regulation complex, NOT5
subunit [Transcription].
Length = 548
Score = 28.5 bits (63), Expect = 3.8
Identities = 31/187 (16%), Positives = 66/187 (35%), Gaps = 28/187 (14%)
Query: 3 WLFGRKITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMESVKIM 62
WL + +++L N+R + M ++ M+ K+ +KE I
Sbjct: 54 WLSKEDVKDKQVLMTNRRLIENGMERFKSVEKLMK---------TKQFSKEALTNPDIID 104
Query: 63 AKDLVRTRKYAKKFMMMKANIQAVSLKIQTLRSQNAMAEAMKGCSRAMQNMNRQMNLPQI 122
K+L + + + + + L+ Q EA + + ++ NL I
Sbjct: 105 PKELKK-----------RDQVLFIHDCLDELQKQLEQYEAQENEEQTERHEFHIANLENI 153
Query: 123 QRILQEFEKQSEIMDMKEEMMNDAMDDAMDADE-DEDETNAVVTQVLDELGLQLGDQLAS 181
+ LQ E M E + + DD E ++D + +++G ++ ++
Sbjct: 154 LKKLQNNE-------MDPEPVEEFQDDIKYYVENNDDPDFIEYDTIYEDMGCEIQPSSSN 206
Query: 182 IPDPASS 188
P
Sbjct: 207 NEAPKEG 213
>gnl|CDD|130146 TIGR01074, rep, ATP-dependent DNA helicase Rep. Designed to
identify rep members of the uvrD/rep subfamily [DNA
metabolism, DNA replication, recombination, and repair].
Length = 664
Score = 28.2 bits (63), Expect = 4.3
Identities = 15/106 (14%), Positives = 42/106 (39%), Gaps = 10/106 (9%)
Query: 68 RTRKYAKKFMMMKANIQAVSLKIQTLRSQNAMAEAMKGCSRAMQNMN-------RQMNLP 120
R + ++F I+ ++ + + + + ++ E + + + R N+
Sbjct: 447 RGYESLQRFTDWLVEIRRLAERSEPIEAVRSLIEDIDYENWLYETSPSPKAAEMRMKNVN 506
Query: 121 QIQRILQEFEKQSEI---MDMKEEMMNDAMDDAMDADEDEDETNAV 163
+ +E + E M + + + + D ++ EDE+E + V
Sbjct: 507 TLFSWFKEMLEGDEEDEPMTLTQVVTRLTLRDMLERGEDEEELDQV 552
>gnl|CDD|235773 PRK06291, PRK06291, aspartate kinase; Provisional.
Length = 465
Score = 28.0 bits (63), Expect = 5.0
Identities = 6/44 (13%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 131 KQSEIMDMKEEMMN---DAMDDAMDADEDEDETNAVVTQVLDEL 171
+++ D ++ A+++A+ + +E + + ++EL
Sbjct: 61 DIAKVKDFIADLRERHYKAIEEAIKDPDIREEVSKTIDSRIEEL 104
>gnl|CDD|202724 pfam03685, UPF0147, Uncharacterized protein family (UPF0147). This
family of small proteins have no known function.
Length = 85
Score = 26.4 bits (59), Expect = 5.1
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 13/55 (23%)
Query: 130 EKQSEIMDMKEEMMND---------AMDDAMDADEDEDETNAV----VTQVLDEL 171
EK + ++M + ++ND A DA A +E+E+ AV +LDE+
Sbjct: 6 EKIKQAIEMLDRIINDTTVPRNIRRAATDAKAALLNEEESPAVRAATAISILDEI 60
>gnl|CDD|227512 COG5185, HEC1, Protein involved in chromosome segregation,
interacts with SMC proteins [Cell division and
chromosome partitioning].
Length = 622
Score = 28.0 bits (62), Expect = 5.2
Identities = 17/147 (11%), Positives = 51/147 (34%), Gaps = 27/147 (18%)
Query: 17 KNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMESVKIMAKDLVRTRKYAKKF 76
+ +++ ++ L + + ++ K + M + + +++ K
Sbjct: 288 QEAMKISQKIKTLREKWRALKSDSNKYENYVNAM--KQKS-------------QEWPGKL 332
Query: 77 MMMKANIQAVSLKIQTLRSQNAMAEAMKGCSRAMQNMNRQMNLPQIQRILQEFEKQSEIM 136
+K+ I+ +I+ L+S Q + ++ Q + + QE EK + +
Sbjct: 333 EKLKSEIELKEEEIKALQSNIDELHK--------QLRKQGISTEQFELMNQEREKLTREL 384
Query: 137 DM----KEEMMNDAMDDAMDADEDEDE 159
D +++ ++A
Sbjct: 385 DKINIQSDKLTKSVKSRKLEAQGIFKS 411
>gnl|CDD|218556 pfam05327, RRN3, RNA polymerase I specific transcription initiation
factor RRN3. This family consists of several eukaryotic
proteins which are homologous to the yeast RRN3 protein.
RRN3 is one of the RRN genes specifically required for
the transcription of rDNA by RNA polymerase I (Pol I) in
Saccharomyces cerevisiae.
Length = 554
Score = 28.0 bits (63), Expect = 5.3
Identities = 13/62 (20%), Positives = 29/62 (46%), Gaps = 2/62 (3%)
Query: 121 QIQRILQEFEKQSEIMDMKEEMMNDAMDDAMDADEDEDETNAVVTQVLDELGLQLGDQLA 180
+IQ L + + + E + +E +D +D M +D+DE + ++ ++L
Sbjct: 217 EIQNELDDIDDEEEERVLADEDDDD--EDDMFDMDDDDEEESDPEVERTSTIKEVSEKLD 274
Query: 181 SI 182
+I
Sbjct: 275 AI 276
>gnl|CDD|227780 COG5493, COG5493, Uncharacterized conserved protein containing a
coiled-coil domain [Function unknown].
Length = 231
Score = 27.5 bits (61), Expect = 5.4
Identities = 16/86 (18%), Positives = 36/86 (41%), Gaps = 5/86 (5%)
Query: 8 KITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMESVKIMAKDLV 67
+I E + + +D++ ++ EQ++K+L AD K ++ + +
Sbjct: 27 EILYEVLAKLTPWQQLATKQDVEELRKETEQRQKEL-ADEKLEVRKQKATKEDLKLLQ-- 83
Query: 68 RTRKYAKKFMMMKANIQAVSLKIQTL 93
R ++F K +I+ + I L
Sbjct: 84 --RFQEEEFRATKEDIKRLETIITGL 107
>gnl|CDD|240197 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal
protein S1 (RPS1) domain. RPS1 is a component of the
small ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria,
the tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain. While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains
have been identified in plants and humans, however
these lack the N-terminal HMBPP reductase domain. This
CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1
homolog. Autoantibodies to double-stranded DNA from
patients with systemic lupus erythematosus cross-react
with the human RPS1 homolog.
Length = 69
Score = 25.7 bits (57), Expect = 5.6
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 35 HMEQQEKKLIADIKKMAKEGQMESVKIMAKD 65
H+ Q K + D+K + KEG VK+++ D
Sbjct: 29 HISQIAHKRVKDVKDVLKEGDKVKVKVLSID 59
>gnl|CDD|219256 pfam06991, Prp19_bind, Splicing factor, Prp19-binding domain. This
family represents the C-terminus (approximately 300
residues) of proteins that are involved as binding
partners for Prp19 as part of the nuclear pore complex.
The family in Drosophila is necessary for pre-mRNA
splicing, and the human protein has been found in
purifications of the spliceosome. In the past this
family was thought, erroneously, to be associated with
microfibrillin.
Length = 277
Score = 27.6 bits (61), Expect = 5.7
Identities = 17/63 (26%), Positives = 37/63 (58%)
Query: 24 KAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMESVKIMAKDLVRTRKYAKKFMMMKANI 83
K R +E++ +EK L + K+ A+E + E++KI+ +++ + + K+ +++ANI
Sbjct: 44 KKDRITIQEREREAAKEKALEEEAKRKAEERKRETLKIVEEEVKKELELKKRNTLLEANI 103
Query: 84 QAV 86
V
Sbjct: 104 DDV 106
>gnl|CDD|239237 cd02911, arch_FMN, Archeal FMN-binding domain. This family of
archaeal proteins are part of the NAD(P)H-dependent
flavin oxidoreductase (oxidored) FMN-binding family that
reduce a range of alternative electron acceptors. Most
use FAD/FMN as a cofactor and NAD(P)H as electron donor.
Some contain 4Fe-4S cluster to transfer electron from
FAD to FMN. The specific function of this group is
unknown.
Length = 233
Score = 27.3 bits (61), Expect = 6.3
Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 4/45 (8%)
Query: 34 QHMEQQEKKLIADIKKMAKEGQMESVKIMA----KDLVRTRKYAK 74
+ + + ++L IK + + G SVKI A D R K
Sbjct: 119 EALLKDPERLSEFIKALKETGVPVSVKIRAGVDVDDEELARLIEK 163
>gnl|CDD|234892 PRK01037, trmD, tRNA (guanine-N(1)-)-methyltransferase/unknown
domain fusion protein; Reviewed.
Length = 357
Score = 27.5 bits (61), Expect = 6.3
Identities = 13/48 (27%), Positives = 19/48 (39%), Gaps = 5/48 (10%)
Query: 30 DREKQHMEQQEKKLIADIKKMAKEGQMESVKIMAKDLVRTRK-YAKKF 76
R + QE K + SV + +DL R +K Y+K F
Sbjct: 226 GRSADCLFTQE----DLPKIEVFSPKTFSVVLEVQDLRRAKKFYSKMF 269
>gnl|CDD|224460 COG1543, COG1543, Uncharacterized conserved protein [Function
unknown].
Length = 504
Score = 27.7 bits (62), Expect = 6.4
Identities = 10/58 (17%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 22 LNKAMRD---LDREKQHMEQQEKKLIADIKKMAKEGQMESVKIMAKDLVRTRKYAKKF 76
L + + D DR +++E + + + K+ A + E + + + R Y +++
Sbjct: 64 LMEMLADPYLQDRYLRYLEWKIELSEKEEKRYADQSLRELAEFYIPEFLNARGYWEQY 121
>gnl|CDD|212549 cd11711, GINS_A_Sld5, Alpha-helical domain of GINS complex
protein Sld5. Sld5 is a component of GINS tetrameric
protein complex, and within the complex Sld5 interacts
with Psf1 via its N-terminal A-domain, and with Psf2
through a combination of the A and B domains. Sld5 in
Drosophila is required for normal cell cycle
progression and the maintenance of genomic integrity.
GINS is a complex of four subunits (Sld5, Psf1, Psf2
and Psf3) that is involved in both initiation and
elongation stages of eukaryotic chromosome replication.
Besides being essential for the maintenance of genomic
integrity, GINS plays a central role in coordinating
DNA replication with cell cycle checkpoints and is
involved in cell growth. The eukaryotic GINS subunits
are homologous and homologs are also found in the
archaea; the complex is not found in bacteria. The four
subunits of the complex consist of two domains each,
termed the alpha-helical (A) and beta-strand (B)
domains. The A and B domains of Sld5/Psf1 are permuted
with respect to Psf1/Psf3.
Length = 119
Score = 26.4 bits (59), Expect = 7.5
Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 7/49 (14%)
Query: 29 LDREKQHMEQQEKKLIA-------DIKKMAKEGQMESVKIMAKDLVRTR 70
++R + +EQQE+ L D++ E ++E ++ + + +RTR
Sbjct: 26 VERVLEQIEQQEENLEELKASEKDDLRLSLHEMELERIRFLLRSYLRTR 74
>gnl|CDD|226889 COG4487, COG4487, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 438
Score = 27.5 bits (61), Expect = 8.2
Identities = 14/57 (24%), Positives = 23/57 (40%)
Query: 12 EEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMESVKIMAKDLVR 68
+ R K L+ E++ E+Q + D++ E Q ES + K L R
Sbjct: 149 KNEERLKFENEKKLEESLELEREKFEEQLHEANLDLEFKENEEQRESKWAILKKLKR 205
>gnl|CDD|172947 PRK14472, PRK14472, F0F1 ATP synthase subunit B; Provisional.
Length = 175
Score = 26.7 bits (59), Expect = 8.7
Identities = 17/52 (32%), Positives = 30/52 (57%), Gaps = 3/52 (5%)
Query: 12 EEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMESVKIMA 63
E +LRKN+ L KA + D+ + ++ +KL A+I + A E+ K++A
Sbjct: 69 EAILRKNRELLAKADAEADKIIREGKEYAEKLRAEITEKA---HTEAKKMIA 117
>gnl|CDD|223778 COG0706, YidC, Preprotein translocase subunit YidC [Intracellular
trafficking and secretion].
Length = 314
Score = 27.0 bits (60), Expect = 8.8
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 103 MKGCSRAMQNMNRQMNLPQIQRILQEFEKQSEIMDMKEEMM 143
+ +R+M M Q P+I+ I QE K ++ ++EMM
Sbjct: 129 SQKSTRSMAKM--QELQPKIKEI-QEKYKGTDKQKQQQEMM 166
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 27.2 bits (61), Expect = 8.9
Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 17/81 (20%)
Query: 1 MEWLFGRKITP------EEMLRKNQRALNKAMRDLDREKQHMEQQE-------KKLIAD- 46
MEWL ++ P E+ + L KA++ L + E E KL+
Sbjct: 327 MEWLKKLEVVPTIRALREQAEDVREEELEKALKKLPNGEDEEEVLEKLARSLVNKLLHAP 386
Query: 47 ---IKKMAKEGQMESVKIMAK 64
+K+ AKEG E ++ + +
Sbjct: 387 TVRLKEAAKEGSEELLRALRE 407
>gnl|CDD|221173 pfam11702, DUF3295, Protein of unknown function (DUF3295). This
family is conserved in fungi but the function is not
known.
Length = 509
Score = 27.2 bits (60), Expect = 9.7
Identities = 9/42 (21%), Positives = 17/42 (40%)
Query: 118 NLPQIQRILQEFEKQSEIMDMKEEMMNDAMDDAMDADEDEDE 159
+L ++ F++Q E +D D ++D DE
Sbjct: 259 SLMSPRKKTASFKEQVVTRTFPERTSDDDEDAIETEEDDVDE 300
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 0.126 0.339
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,977,272
Number of extensions: 1125854
Number of successful extensions: 1967
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1899
Number of HSP's successfully gapped: 189
Length of query: 237
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 143
Effective length of database: 6,768,326
Effective search space: 967870618
Effective search space used: 967870618
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 (21.9 bits)
S2: 57 (25.6 bits)