RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16497
(143 letters)
>gnl|CDD|216288 pfam01079, Hint, Hint module. This is an alignment of the Hint
module in the Hedgehog proteins. It does not include any
Inteins which also possess the Hint module.
Length = 214
Score = 147 bits (374), Expect = 8e-46
Identities = 61/137 (44%), Positives = 81/137 (59%), Gaps = 4/137 (2%)
Query: 2 TPSHLILRWHRPNAKSILSDIEYTYAERVRVNDSIIVHKNGKAYV--ERVTRLENVIQTG 59
TP+HLI S + E +A VR D ++V NG + +V R+ V +TG
Sbjct: 80 TPAHLIFVADCNTTSS--ALFEAVFASDVRPGDYVLVQDNGGGGLRPVKVVRVTTVERTG 137
Query: 60 VYAPLTTSGTIVVNNVFASCYAVIDNQFLAHLSFIPVRLYHSLVNLFSSNHIENSSHVTG 119
VYAPLT GTIVV+ V ASCYAVI++ LAH +F PVRL HSL +L + ++S G
Sbjct: 138 VYAPLTAHGTIVVDGVLASCYAVIESHSLAHWAFAPVRLLHSLSSLLWPSPSSSTSQQEG 197
Query: 120 IHWYPKLLYSMSDYFIP 136
+HWY KLLY + Y +P
Sbjct: 198 VHWYAKLLYRIGTYVLP 214
>gnl|CDD|238035 cd00081, Hint, Hedgehog/Intein domain, found in Hedgehog proteins
as well as proteins which contain inteins and undergo
protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In
protein splicing an intervening polypeptide sequence -
the intein - is excised from a protein, and the flanking
polypeptide sequences - the exteins - are joined by a
peptide bond. In addition to the autocatalytic splicing
domain, many inteins contain an inserted endonuclease
domain, which plays a role in spreading inteins.
Hedgehog proteins are a major class of intercellular
signaling molecules, which control inductive
interactions during animal development. The mature
signaling forms of hedgehog proteins are the N-terminal
fragments, which are covalently linked to cholesterol at
their C-termini. This modification is the result of an
autoprocessing step catalyzed by the C-terminal
fragments, which are aligned here.
Length = 136
Score = 43.0 bits (102), Expect = 4e-06
Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 12/79 (15%)
Query: 2 TPSHLILRWHRPNAKSILSDIEYTYAERVRVNDSIIVHKNGKAYVERVTRLENVIQTGVY 61
TP HL+ ++++ +A ++ D ++V V+ + +E GVY
Sbjct: 69 TPDHLLFVL-EDG------ELKWVFASDLKPGDYVLVPV--LEKVKEIEEIEY--TGGVY 117
Query: 62 APLTTS-GTIVVNNVFASC 79
+ N V
Sbjct: 118 DLTVEDNHNFIANGVLVHN 136
>gnl|CDD|197641 smart00305, HintC, Hint (Hedgehog/Intein) domain C-terminal
region. Hedgehog/Intein domain, C-terminal region.
Domain has been split to accommodate large insertions
of endonucleases.
Length = 46
Score = 37.9 bits (89), Expect = 7e-05
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 41 NGKAYVERVTRLENVIQTGVYAP-LTTSGTIVVNNVFASCYAVID 84
G RV +E TGVY P +T + + N + A I+
Sbjct: 1 EGDFRFVRVKSIEETEYTGVYDPTVTENHNFIANGILVHNCAEIE 45
>gnl|CDD|215848 pfam00306, ATP-synt_ab_C, ATP synthase alpha/beta chain, C
terminal domain.
Length = 110
Score = 29.2 bits (66), Expect = 0.39
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 1/46 (2%)
Query: 43 KAYVERVTRLENVIQTGVYAPLTTSGTIV-VNNVFASCYAVIDNQF 87
K +ER R+E ++ Y+P V V YA++ +F
Sbjct: 34 KLTLERARRIEEFLKQNQYSPEPVEKQYVPVEETIDLFYALLRGKF 79
>gnl|CDD|217388 pfam03144, GTP_EFTU_D2, Elongation factor Tu domain 2.
Elongation factor Tu consists of three structural
domains, this is the second domain. This domain adopts
a beta barrel structure. This the second domain is
involved in binding to charged tRNA. This domain is
also found in other proteins such as elongation factor
G and translation initiation factor IF-2. This domain
is structurally related to pfam03143, and in fact has
weak sequence matches to this domain.
Length = 70
Score = 28.4 bits (64), Expect = 0.39
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 30 VRVNDSIIVHKNGKAYVERVTRLEN 54
++ D +++ NG RVT LE
Sbjct: 13 LKKGDKVVIGPNGTGKKGRVTSLEM 37
>gnl|CDD|99708 cd00004, Sortase, Sortases are cysteine transpeptidases, found in
gram-positive bacteria, that anchor surface proteins to
peptidoglycans of the bacterial cell wall envelope. They
do so by catalyzing a transpeptidation reaction in which
the surface protein substrate is cleaved at a conserved
cell wall sorting signal and covalently linked to
peptidoglycan for display on the bacterial surface.
Sortases are grouped into different classes and
subfamilies based on sequence, membrane topology,
genomic positioning, and cleavage site preference. The
different classes are called Sortase A or SrtA
(subfamily 1), B or SrtB (subfamily 2), C or SrtC
(subfamily3), D or SrtD (subfamilies 4 and 5), and E or
SrtE. In two different sortase subfamilies, the
N-terminus either functions as both a signal peptide for
secretion and a stop-transfer signal for membrane
anchoring, or it contains a signal peptide only and the
C-terminus serves as a membrane anchor. Most
gram-positive bacteria contain more than one sortase and
it is thought that the different sortases anchor
different surface protein classes. The sortase domain is
a modified beta-barrel flanked by two (SrtA) or three
(SrtB) short alpha-helices.
Length = 128
Score = 28.8 bits (65), Expect = 0.56
Identities = 12/42 (28%), Positives = 19/42 (45%)
Query: 28 ERVRVNDSIIVHKNGKAYVERVTRLENVIQTGVYAPLTTSGT 69
+ ++ D I + GK YV +VT + V T V +G
Sbjct: 63 DNLKKGDKIYLTDGGKTYVYKVTSILTVTPTDVVVVNPPTGD 104
>gnl|CDD|213282 cd05914, FACL_like_3, Uncharacterized subfamily of fatty acid CoA
ligase (FACL). Fatty acyl-CoA ligases catalyze the
ATP-dependent activation of fatty acids in a two-step
reaction. The carboxylate substrate first reacts with
ATP to form an acyl-adenylate intermediate, which then
reacts with CoA to produce an acyl-CoA ester. This is a
required step before free fatty acids can participate in
most catabolic and anabolic reactions.
Length = 448
Score = 29.5 bits (67), Expect = 0.60
Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 50 TRLENVIQTGVYAPLTTSGTIVV 72
T LEN+ GVYAPL T+++
Sbjct: 164 TLLENI--AGVYAPLLMGATVIL 184
>gnl|CDD|99713 cd05830, Sortase_D_5, Sortase D (SrtD) is a membrane
transpeptidase found in gram-positive bacteria that
anchors surface proteins to peptidoglycans of the
bacterial cell wall envelope. This involves a
transpeptidation reaction in which the surface protein
substrate is cleaved at the cell wall sorting signal
and covalently linked to peptidoglycan for display on
the bacterial surface. Sortases are grouped into
different classes and subfamilies based on sequence,
membrane topology, genomic positioning, and cleavage
site preference. Class D sortases are further
classified into subfamilies 4 and 5. This group
contains a subset of Class D sortases belonging to
subfamily-5 represented by Streptomyces avermitilis
SAV4337. Subfamily-5 sortases recognize a nonstandard
sorting signal (LAXTG) and have replaced Sortase A in
some gram-postive bacteria. They may play a
housekeeping role in the cell.
Length = 137
Score = 26.1 bits (58), Expect = 4.8
Identities = 10/33 (30%), Positives = 14/33 (42%)
Query: 29 RVRVNDSIIVHKNGKAYVERVTRLENVIQTGVY 61
++R D I+V Y V E V+ T V
Sbjct: 65 KLRPGDKIVVETADGWYTYVVRSSEIVLPTDVE 97
>gnl|CDD|197642 smart00306, HintN, Hint (Hedgehog/Intein) domain N-terminal region.
Hedgehog/Intein domain, N-terminal region. Domain has
been split to accommodate large insertions of
endonucleases.
Length = 100
Score = 25.7 bits (57), Expect = 5.5
Identities = 9/39 (23%), Positives = 18/39 (46%), Gaps = 7/39 (17%)
Query: 2 TPSHLILRWHRPNAKSILSDIEYTYAERVRVNDSIIVHK 40
TP HL+L R + + +A ++ D ++V +
Sbjct: 69 TPDHLLLV--RDG-----GKLVWVFASELKPGDYVLVPR 100
>gnl|CDD|226666 COG4209, LplB, ABC-type polysaccharide transport system, permease
component [Carbohydrate transport and metabolism].
Length = 309
Score = 26.1 bits (58), Expect = 7.0
Identities = 17/51 (33%), Positives = 21/51 (41%), Gaps = 2/51 (3%)
Query: 51 RLENVIQTGVYAPLTTSGTIVVNNVFA--SCYAVIDNQFLAHLSFIPVRLY 99
+ V+QT Y P S +V VFA S I NQ L L P+
Sbjct: 113 VFKKVVQTISYLPHFLSWVVVSGFVFAFLSIDGGIINQLLMSLGGDPINFL 163
>gnl|CDD|191263 pfam05368, NmrA, NmrA-like family. NmrA is a negative
transcriptional regulator involved in the
post-translational modification of the transcription
factor AreA. NmrA is part of a system controlling
nitrogen metabolite repression in fungi. This family
only contains a few sequences as iteration results in
significant matches to other Rossmann fold families.
Length = 232
Score = 25.7 bits (57), Expect = 8.3
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 28 ERVRVNDSIIVHKNGKAYVERVTRLENVIQTGVYAPL 64
+R + + H + KA VER R + T VYA
Sbjct: 108 DRSNGVEPAVPHFDSKAEVERYIRALGIPYTFVYAGF 144
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
0.322 0.134 0.412
Gapped
Lambda K H
0.267 0.0750 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,317,890
Number of extensions: 636689
Number of successful extensions: 523
Number of sequences better than 10.0: 1
Number of HSP's gapped: 519
Number of HSP's successfully gapped: 21
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
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 (21.9 bits)
S2: 54 (24.5 bits)