RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4956
(361 letters)
>gnl|CDD|200951 pfam00041, fn3, Fibronectin type III domain.
Length = 84
Score = 50.5 bits (121), Expect = 3e-08
Identities = 21/85 (24%), Positives = 29/85 (34%), Gaps = 3/85 (3%)
Query: 186 PGKFIVWFRNETTLLVLWQPSYPASIYTHYKVSIDPPDAPESVLYVEKEGEPPGPAQAAF 245
P V T+L + W P T Y+V P + E + P
Sbjct: 3 PTNLTVTDVTSTSLTLSWSPPPGNGPITGYEVEYRPVNGGEEWKEIT---VPGTTTSYTL 59
Query: 246 KGLVPGRAYNISVQTVSEDEISTPT 270
GL PG Y + VQ V+ P+
Sbjct: 60 TGLKPGTEYEVRVQAVNGAGEGPPS 84
Score = 44.0 bits (104), Expect = 5e-06
Identities = 21/71 (29%), Positives = 29/71 (40%), Gaps = 2/71 (2%)
Query: 290 SITSNSLRVVWEPPKGFSEFDKYQVSINVRRPGASSTPITKSRDEPTQCDMSEGLEPGRT 349
+TS SL + W PP G Y+V R + T GL+PG
Sbjct: 10 DVTSTSLTLSWSPPPGNGPITGYEVE--YRPVNGGEEWKEITVPGTTTSYTLTGLKPGTE 67
Query: 350 YQVLVKTVSGK 360
Y+V V+ V+G
Sbjct: 68 YEVRVQAVNGA 78
Score = 41.6 bits (98), Expect = 3e-05
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 2/78 (2%)
Query: 91 DPPTNLSVNVRSGKTAQIFWSPP-ISGKYSGFKLKVISLSEKTPPRIIGFTENPPAGYSL 149
PTNL+V + + + WSPP +G +G++++ ++ + I Y+L
Sbjct: 1 SAPTNLTVTDVTSTSLTLSWSPPPGNGPITGYEVEYRPVNGGEEWKEI-TVPGTTTSYTL 59
Query: 150 KDLTPGGSYQVQLFSVYD 167
L PG Y+V++ +V
Sbjct: 60 TGLKPGTEYEVRVQAVNG 77
>gnl|CDD|238020 cd00063, FN3, Fibronectin type 3 domain; One of three types of
internal repeats found in the plasma protein
fibronectin. Its tenth fibronectin type III repeat
contains an RGD cell recognition sequence in a flexible
loop between 2 strands. Approximately 2% of all animal
proteins contain the FN3 repeat; including extracellular
and intracellular proteins, membrane spanning cytokine
receptors, growth hormone receptors, tyrosine
phosphatase receptors, and adhesion molecules. FN3-like
domains are also found in bacterial glycosyl hydrolases.
Length = 93
Score = 46.3 bits (110), Expect = 9e-07
Identities = 25/94 (26%), Positives = 40/94 (42%), Gaps = 3/94 (3%)
Query: 90 PDPPTNLSVNVRSGKTAQIFWSPP--ISGKYSGFKLKVISLSEKTPPRIIGFTENPPAGY 147
P PPTNL V + + + W+PP G +G+ ++ + + T Y
Sbjct: 1 PSPPTNLRVTDVTSTSVTLSWTPPEDDGGPITGYVVEYREKGSGDW-KEVEVTPGSETSY 59
Query: 148 SLKDLTPGGSYQVQLFSVYDSKESVAYTSRNFTT 181
+L L PG Y+ ++ +V ES S TT
Sbjct: 60 TLTGLKPGTEYEFRVRAVNGGGESPPSESVTVTT 93
Score = 40.9 bits (96), Expect = 6e-05
Identities = 19/90 (21%), Positives = 28/90 (31%), Gaps = 4/90 (4%)
Query: 183 PNTPGKFIVWFRNETTLLVLWQ-PSYPASIYTHYKVSIDPPDAPESVLYVEKEGEPPGPA 241
P+ P V T++ + W P T Y V + + G
Sbjct: 1 PSPPTNLRVTDVTSTSVTLSWTPPEDDGGPITGYVVEYREKGSGDWKEVEVTPGSET--- 57
Query: 242 QAAFKGLVPGRAYNISVQTVSEDEISTPTT 271
GL PG Y V+ V+ S P+
Sbjct: 58 SYTLTGLKPGTEYEFRVRAVNGGGESPPSE 87
Score = 37.1 bits (86), Expect = 0.001
Identities = 18/72 (25%), Positives = 31/72 (43%), Gaps = 3/72 (4%)
Query: 290 SITSNSLRVVWEPPKG-FSEFDKYQVSINVRRPGASSTPITKSRDEPTQCDMSEGLEPGR 348
+TS S+ + W PP+ Y V + G + + T ++ GL+PG
Sbjct: 11 DVTSTSVTLSWTPPEDDGGPITGYVVEYREKGSGDWKE-VEVTPGSETSYTLT-GLKPGT 68
Query: 349 TYQVLVKTVSGK 360
Y+ V+ V+G
Sbjct: 69 EYEFRVRAVNGG 80
>gnl|CDD|214495 smart00060, FN3, Fibronectin type 3 domain. One of three types of
internal repeat within the plasma protein, fibronectin.
The tenth fibronectin type III repeat contains a RGD
cell recognition sequence in a flexible loop between 2
strands. Type III modules are present in both
extracellular and intracellular proteins.
Length = 83
Score = 41.8 bits (98), Expect = 2e-05
Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 1/83 (1%)
Query: 90 PDPPTNLSVNVRSGKTAQIFWSPPISGKYSGFKLKVISLSEKTPPRIIGFTENPPA-GYS 148
P PP+NL V + + + W PP +G+ + + P + Y+
Sbjct: 1 PSPPSNLRVTDVTSTSVTLSWEPPPDDGITGYIVGYRVEYREEGSEWKEVNVTPSSTSYT 60
Query: 149 LKDLTPGGSYQVQLFSVYDSKES 171
L L PG Y+ ++ +V + E
Sbjct: 61 LTGLKPGTEYEFRVRAVNGAGEG 83
Score = 36.8 bits (85), Expect = 0.002
Identities = 19/71 (26%), Positives = 28/71 (39%), Gaps = 1/71 (1%)
Query: 290 SITSNSLRVVWEPPKGFSEFDKYQVSINVRRPGASSTPITKSRDEPTQCDMSEGLEPGRT 349
+TS S+ + WEPP Y V V S + + GL+PG
Sbjct: 11 DVTSTSVTLSWEPPPD-DGITGYIVGYRVEYREEGSEWKEVNVTPSSTSYTLTGLKPGTE 69
Query: 350 YQVLVKTVSGK 360
Y+ V+ V+G
Sbjct: 70 YEFRVRAVNGA 80
Score = 32.2 bits (73), Expect = 0.059
Identities = 20/85 (23%), Positives = 28/85 (32%), Gaps = 2/85 (2%)
Query: 183 PNTPGKFIVWFRNETTLLVLWQPSYPASIYTHYKVSIDPPDAPESVLYVEKEGEPPGPAQ 242
P+ P V T++ + W+P I T Y V E + E P
Sbjct: 1 PSPPSNLRVTDVTSTSVTLSWEPPPDDGI-TGYIVGYRVEYREEGSEWKEVNVTPSST-S 58
Query: 243 AAFKGLVPGRAYNISVQTVSEDEIS 267
GL PG Y V+ V+
Sbjct: 59 YTLTGLKPGTEYEFRVRAVNGAGEG 83
>gnl|CDD|187589 cd05328, 3alpha_HSD_SDR_c, alpha hydroxysteroid dehydrogenase
(3alpha_HSD), classical (c) SDRs. Bacterial
3-alpha_HSD, which catalyzes the NAD-dependent
oxidoreduction of hydroxysteroids, is a dimeric member
of the classical SDR family. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 29.0 bits (65), Expect = 3.0
Identities = 14/71 (19%), Positives = 21/71 (29%), Gaps = 10/71 (14%)
Query: 223 DAPESVLYVEKEGEPPGPAQAAFKGLV----------PGRAYNISVQTVSEDEISTPTTA 272
+V E G+P A A K + + V TV+ + TP
Sbjct: 132 TEARAVALAEHAGQPGYLAYAGSKEALTVWTRRRAATWLYGAGVRVNTVAPGPVETPILQ 191
Query: 273 QYRTIPLRPLS 283
+ P S
Sbjct: 192 AFLQDPRGGES 202
>gnl|CDD|240301 PTZ00166, PTZ00166, DNA polymerase delta catalytic subunit;
Provisional.
Length = 1054
Score = 29.2 bits (66), Expect = 4.7
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 179 FTTK--PNTPGKFIVWFRNETTLLVLW 203
FT K + G ++ F E LL+ W
Sbjct: 311 FTLKECASIAGANVLSFETEKELLLAW 337
>gnl|CDD|237187 PRK12743, PRK12743, oxidoreductase; Provisional.
Length = 256
Score = 27.7 bits (62), Expect = 8.0
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 5/38 (13%)
Query: 241 AQAAFKGLVPGRA-----YNISVQTVSEDEISTPTTAQ 273
A+ A GL A + I V V+ I+TP
Sbjct: 156 AKHALGGLTKAMALELVEHGILVNAVAPGAIATPMNGM 193
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
0.313 0.133 0.403
Gapped
Lambda K H
0.267 0.0591 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,444,206
Number of extensions: 1722257
Number of successful extensions: 1043
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1036
Number of HSP's successfully gapped: 17
Length of query: 361
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 263
Effective length of database: 6,590,910
Effective search space: 1733409330
Effective search space used: 1733409330
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: 60 (27.2 bits)