RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1724
(473 letters)
>gnl|CDD|217391 pfam03152, UFD1, Ubiquitin fusion degradation protein UFD1.
Post-translational ubiquitin-protein conjugates are
recognised for degradation by the ubiquitin fusion
degradation (UFD) pathway. Several proteins involved in
this pathway have been identified. This family includes
UFD1, a 40kD protein that is essential for vegetative
cell viability. The human UFD1 gene is expressed at high
levels during embryogenesis, especially in the eyes and
in the inner ear primordia and is thought to be
important in the determination of ectoderm-derived
structures, including neural crest cells. In addition,
this gene is deleted in the CATCH-22 (cardiac defects,
abnormal facies, thymic hypoplasia, cleft palate and
hypocalcaemia with deletions on chromosome 22) syndrome.
This clinical syndrome is associated with a variety of
developmental defects, all characterized by
microdeletions on 22q11.2. Two such developmental
defects are the DiGeorge syndrome OMIM:188400, and the
velo-cardio- facial syndrome OMIM:145410. Several of the
abnormalities associated with these conditions are
thought to be due to defective neural crest cell
differentiation.
Length = 176
Score = 307 bits (790), Expect = e-104
Identities = 116/176 (65%), Positives = 142/176 (80%)
Query: 209 PFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRIT 268
F ++Y+C+ VS PGNERED+E GGKII+PPSAL++L+RLNI YPMLF+L N ++T
Sbjct: 1 RFEQTYRCYPVSFLPGNEREDIEYGGKIILPPSALDRLSRLNIEYPMLFELQNPANKKVT 60
Query: 269 HSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLDITNP 328
H GVLEF+A+EG +YLPYWMM+NL L+EG+LV I S SLP TF K QPQ+ DFLDI+NP
Sbjct: 61 HCGVLEFIAEEGTIYLPYWMMQNLGLEEGDLVQITSASLPKGTFVKLQPQSTDFLDISNP 120
Query: 329 KAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTIIECDMNVDFAPP 384
KAVLEN LRNF+ LT GD I INYN KIYE+ +LE KP NA++IIE D+ VDFAPP
Sbjct: 121 KAVLENALRNFSTLTKGDTIVINYNDKIYEIDILEVKPANAISIIETDLEVDFAPP 176
Score = 138 bits (350), Expect = 8e-39
Identities = 50/81 (61%), Positives = 65/81 (80%)
Query: 8 PFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRIT 67
F ++Y+C+ VS PGNERED+E GGKII+PPSAL++L+RLNI YPMLF+L N ++T
Sbjct: 1 RFEQTYRCYPVSFLPGNEREDIEYGGKIILPPSALDRLSRLNIEYPMLFELQNPANKKVT 60
Query: 68 HSGVLEFVADEGKVYLPYWCF 88
H GVLEF+A+EG +YLPYW
Sbjct: 61 HCGVLEFIAEEGTIYLPYWMM 81
Score = 104 bits (262), Expect = 3e-26
Identities = 40/62 (64%), Positives = 49/62 (79%)
Query: 84 PYWCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGV 143
Y C+ VS PGNERED+E GGKII+PPSAL++L+RLNI YPMLF+L N ++TH GV
Sbjct: 5 TYRCYPVSFLPGNEREDIEYGGKIILPPSALDRLSRLNIEYPMLFELQNPANKKVTHCGV 64
Query: 144 LE 145
LE
Sbjct: 65 LE 66
>gnl|CDD|227469 COG5140, UFD1, Ubiquitin fusion-degradation protein
[Posttranslational modification, protein turnover,
chaperones].
Length = 331
Score = 227 bits (579), Expect = 1e-70
Identities = 92/210 (43%), Positives = 130/210 (61%), Gaps = 4/210 (1%)
Query: 191 SAHKEFQFGFNMFPDIPRPFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLN 250
S F G D+ + F +C+ +M R++ GGK+I+PPSAL +L+ LN
Sbjct: 3 SGFSSFGGGNGFLNDLFQLFGEKPRCYPRAMKFDGCRQNANFGGKVILPPSALVKLSSLN 62
Query: 251 ICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVA 310
I YPMLF++++ TH GVLEF+A+EG+VYLP WMM+ L ++ G+LV + P+
Sbjct: 63 IQYPMLFEISHSDGIYRTHGGVLEFIAEEGRVYLPSWMMQTLSMEPGDLVVLRYTDFPLG 122
Query: 311 TFSKFQPQTCDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKP---G 367
F K PQ+ DFLDI +PKAVLENCLRNF+ LT GD I I YN ++ + P
Sbjct: 123 KFVKLIPQSVDFLDIEDPKAVLENCLRNFSTLTEGDEIEIQYNDEVGSIKFTVVHPEPSA 182
Query: 368 NAVTIIECDMNVDFAPPVGYTEP-EKVKEK 396
NA+ ++E D+ VDF PP+GY E ++ KE+
Sbjct: 183 NAIYVVETDLVVDFLPPIGYKEKAQQDKER 212
Score = 113 bits (283), Expect = 7e-28
Identities = 42/97 (43%), Positives = 63/97 (64%), Gaps = 1/97 (1%)
Query: 1 MFPDIPRPFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTN 60
D+ + F +C+ +M R++ GGK+I+PPSAL +L+ LNI YPMLF++++
Sbjct: 14 FLNDLFQLFGEKPRCYPRAMKFDGCRQNANFGGKVILPPSALVKLSSLNIQYPMLFEISH 73
Query: 61 QKMGRITHSGVLEFVADEGKVYLPYWCF-SVSMFPGN 96
TH GVLEF+A+EG+VYLP W ++SM PG+
Sbjct: 74 SDGIYRTHGGVLEFIAEEGRVYLPSWMMQTLSMEPGD 110
Score = 80.0 bits (197), Expect = 2e-16
Identities = 27/65 (41%), Positives = 40/65 (61%)
Query: 85 YWCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVL 144
C+ +M R++ GGK+I+PPSAL +L+ LNI YPMLF++++ TH GVL
Sbjct: 26 PRCYPRAMKFDGCRQNANFGGKVILPPSALVKLSSLNIQYPMLFEISHSDGIYRTHGGVL 85
Query: 145 ELDGK 149
E +
Sbjct: 86 EFIAE 90
>gnl|CDD|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional.
Length = 567
Score = 116 bits (292), Expect = 6e-28
Identities = 70/199 (35%), Positives = 104/199 (52%), Gaps = 22/199 (11%)
Query: 233 GGKIIMPPSALEQLTRLNIC--YPMLFKLT-----------NQKMGRITHSGVLEFVADE 279
G KI +PPS +L+ P+ F+L+ + + THSGVLEF A+E
Sbjct: 91 GDKIKLPPSCFTELSDQGAFDKGPLYFRLSVVHQEGSGEMKDTDSQKTTHSGVLEFTAEE 150
Query: 280 GKVYLPYWMMRNLLLD---EGELVNIESVSLPVATFSKFQPQTCDFLDITNPKAVLENCL 336
G V LP + NL + LV + + LP T++K QP F D+ N KAVLE L
Sbjct: 151 GSVGLPPHVWSNLFPSDPPDVPLVEVRYIWLPKGTYAKLQPDGVGFSDLPNHKAVLETAL 210
Query: 337 RNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTIIECDMNVDFAPPVGYTEPEKVKEK 396
R A L+ D++ +NY Y+L VLE KP ++V+++E D+ VD VG P+ V +
Sbjct: 211 RQHATLSEDDVLVVNYGQLTYKLKVLELKPASSVSVLETDIEVDI---VG---PDSVSNE 264
Query: 397 EEDNMIDPVDLMPEPSGFV 415
E +++ P++ SG V
Sbjct: 265 ENQHVLKPLEFGKSESGMV 283
Score = 42.6 bits (100), Expect = 4e-04
Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 14/78 (17%)
Query: 32 GGKIIMPPSALEQLTRLNIC--YPMLFKLT-----------NQKMGRITHSGVLEFVADE 78
G KI +PPS +L+ P+ F+L+ + + THSGVLEF A+E
Sbjct: 91 GDKIKLPPSCFTELSDQGAFDKGPLYFRLSVVHQEGSGEMKDTDSQKTTHSGVLEFTAEE 150
Query: 79 GKVYLPYWCFSVSMFPGN 96
G V LP +S ++FP +
Sbjct: 151 GSVGLPPHVWS-NLFPSD 167
>gnl|CDD|129147 TIGR00036, dapB, dihydrodipicolinate reductase. [Amino acid
biosynthesis, Aspartate family].
Length = 266
Score = 33.5 bits (77), Expect = 0.18
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 295 DEGELVNIESVSLPVATFSKFQPQTCD-FLDITNPKAVLEN 334
D GEL I V +PV + D +D T P+ VL +
Sbjct: 44 DAGELAGIGKVGVPVTDDLEAVETDPDVLIDFTTPEGVLNH 84
>gnl|CDD|202475 pfam02933, CDC48_2, Cell division protein 48 (CDC48), domain 2.
This domain has a double psi-beta barrel fold and
includes VCP-like ATPase and N-ethylmaleimide sensitive
fusion protein N-terminal domains. Both the VAT and NSF
N-terminal functional domains consist of two structural
domains of which this is at the C-terminus. The VAT-N
domain found in AAA ATPases pfam00004 is a substrate
185-residue recognition domain.
Length = 61
Score = 29.4 bits (67), Expect = 0.49
Identities = 10/45 (22%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 330 AVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTIIE 374
A + ++ G I ++ K+ L V+ T+P V + E
Sbjct: 8 AYFKRQFEGQP-VSKGQTIVFDFLGKLLPLVVVSTEPSGPVIVTE 51
>gnl|CDD|218398 pfam05045, RgpF, Rhamnan synthesis protein F. This family consists
of a group of proteins which are related to the
Streptococcus rhamnose-glucose polysaccharide assembly
protein (RgpF). Rhamnan backbones are found in several O
polysaccharides of phytopathogenic bacteria and are
regarded as pathogenic factors.
Length = 498
Score = 29.3 bits (66), Expect = 4.3
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 312 FSKFQPQTCDFLDITNPKAVLEN 334
F + + + CDF ITN +A+ N
Sbjct: 73 FEEMERRDCDFWGITNHRAIKPN 95
>gnl|CDD|222973 PHA03081, PHA03081, putative metalloprotease; Provisional.
Length = 595
Score = 28.8 bits (65), Expect = 8.5
Identities = 28/115 (24%), Positives = 41/115 (35%), Gaps = 32/115 (27%)
Query: 10 NRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHS 69
N + C V F G D+ GG+I M L+ L + ML +M RI+
Sbjct: 119 NEVFHCMDVLTFLGGG--DLYNGGRIDM----LDNLNDVRD---MLSN----RMHRISGP 165
Query: 70 GVLEFVADEGKVYLPYWCFSV------------SMFPGNEREDVERGGKIIMPPS 112
++ FV + S+ P + GGKI+M PS
Sbjct: 166 NIVIFVKELNPN-----TLSLLNNTFGTLPSCPETIPPPILVSI--GGKIVMMPS 213
>gnl|CDD|227268 COG4932, COG4932, Predicted outer membrane protein [Cell envelope
biogenesis, outer membrane].
Length = 1531
Score = 28.7 bits (64), Expect = 8.7
Identities = 17/63 (26%), Positives = 25/63 (39%), Gaps = 7/63 (11%)
Query: 126 MLFKLTNQKMGRITHSGVLELDGKRKKKDTVETGGTPTK--REYQRGIPH-----YDYEP 178
+ FK +IT+ + G R K+ V T G R Q+ + DYE
Sbjct: 504 LQFKEDIDNAYKITYQTKVTDFGNRTIKNEVTTEGVSASANRAIQQDLLKKEAGDIDYEN 563
Query: 179 NTL 181
NT+
Sbjct: 564 NTM 566
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
0.320 0.139 0.424
Gapped
Lambda K H
0.267 0.0658 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,613,878
Number of extensions: 2404235
Number of successful extensions: 1527
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1523
Number of HSP's successfully gapped: 19
Length of query: 473
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 373
Effective length of database: 6,502,202
Effective search space: 2425321346
Effective search space used: 2425321346
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (27.4 bits)