RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12348
(178 letters)
>gnl|CDD|214550 smart00194, PTPc, Protein tyrosine phosphatase, catalytic domain.
Length = 259
Score = 145 bits (369), Expect = 5e-44
Identities = 54/142 (38%), Positives = 71/142 (50%), Gaps = 3/142 (2%)
Query: 31 WTMGFSNEAEYIAAQGPKADTVADFWTMVLQHQVVKIVMLCSFVEKGRVKCEKYFPDRVN 90
+ G + YIA QGP TV DFW MV + +V IVML VEKGR KC +Y+PD
Sbjct: 61 YIDGPNGPKAYIATQGPLPSTVEDFWRMVWEQKVTVIVMLTELVEKGREKCAQYWPDEEG 120
Query: 91 EYFVFNNIRVGCTEQEVGSHHTCTHLRITR--DSEVLEVKHFHLHDWQDFSIPGGPDVLV 148
E + +I V E +T L +T SE V H+H +W D +P P+ ++
Sbjct: 121 EPLTYGDITVTLKSVEKVDDYTIRTLEVTNTGCSETRTVTHYHYTNWPDHGVPESPESIL 180
Query: 149 NFCHLVRNSTPTSQLS-VVHCR 169
+ VR S TS VVHC
Sbjct: 181 DLIRAVRKSQSTSTGPIVVHCS 202
>gnl|CDD|215717 pfam00102, Y_phosphatase, Protein-tyrosine phosphatase.
Length = 233
Score = 139 bits (352), Expect = 1e-41
Identities = 47/143 (32%), Positives = 66/143 (46%), Gaps = 5/143 (3%)
Query: 33 MGFSNEAEYIAAQGPKADTVADFWTMVLQHQVVKIVMLCSFVEKGRVKCEKYFPDRVNEY 92
G+ +IA QGP +T+ DFW MV + +V IVML EKGR KC++Y+P+
Sbjct: 35 DGYRKPRAFIATQGPLPNTIEDFWRMVWEQKVTTIVMLTELEEKGREKCDQYWPEEEEGS 94
Query: 93 FVFNNIRVGCT-EQEVGSHHTCTHLRITRD--SEVLEVKHFHLHDWQDFSIPGGPDVLVN 149
+ +I V E+E +T + E V HFH W D +P P L++
Sbjct: 95 LTYGDISVTLVKEEEEEDDYTVRTFELKNGGSEETRTVTHFHYTGWPDHGVPESPKSLLD 154
Query: 150 FCHLVRNSTPTSQLS--VVHCRH 170
VR S + VVHC
Sbjct: 155 LIRKVRKSQADPRSGPIVVHCSA 177
>gnl|CDD|238006 cd00047, PTPc, Protein tyrosine phosphatases (PTP) catalyze the
dephosphorylation of phosphotyrosine peptides; they
regulate phosphotyrosine levels in signal transduction
pathways. The depth of the active site cleft renders the
enzyme specific for phosphorylated Tyr (pTyr) residues,
instead of pSer or pThr. This family has a distinctive
active site signature motif, HCSAGxGRxG. Characterized
as either transmembrane, receptor-like or
non-transmembrane (soluble) PTPs. Receptor-like PTP
domains tend to occur in two copies in the cytoplasmic
region of the transmembrane proteins, only one copy may
be active.
Length = 231
Score = 138 bits (349), Expect = 3e-41
Identities = 50/142 (35%), Positives = 69/142 (48%), Gaps = 5/142 (3%)
Query: 31 WTMGFSNEAEYIAAQGPKADTVADFWTMVLQHQVVKIVMLCSFVEKGRVKCEKYFPDRVN 90
+ G++ YIA QGP +TV DFW MV + +V IVML VEKGR KC +Y+P+
Sbjct: 33 YIDGYNPPKAYIATQGPLPNTVEDFWRMVWEQKVPVIVMLTELVEKGREKCAQYWPEEEG 92
Query: 91 EYFVFNNIRVGCTEQEVGSHHTCTHLRITR--DSEVLEVKHFHLHDWQDFSIPGGPDVLV 148
+ +I V +E +T L+++ E V HF W D +P PD L+
Sbjct: 93 SL-TYGDITVTLVSEEKLDDYTVRTLKLSNTGTGETRTVTHFQYTGWPDHGVPESPDSLL 151
Query: 149 NFCHLVRNSTPTSQLS--VVHC 168
+ VR S VVHC
Sbjct: 152 DLLRKVRKSQQQPGSGPIVVHC 173
>gnl|CDD|222923 PHA02738, PHA02738, hypothetical protein; Provisional.
Length = 320
Score = 73.0 bits (179), Expect = 8e-16
Identities = 38/123 (30%), Positives = 54/123 (43%), Gaps = 1/123 (0%)
Query: 34 GFSNEAEYIAAQGPKADTVADFWTMVLQHQVVKIVMLCSFVEKGRVKCEKYFPDRVNEYF 93
GF + ++I Q P T DF+ M+ V IVMLC E GR KC Y+ D
Sbjct: 85 GFEYKKKFICGQAPTRQTCYDFYRMLWMEHVQIIVMLCKKKENGREKCFPYWSDVEQGSI 144
Query: 94 VFNNIRVGCTEQEVGSHHTCTHLRITRDSEVL-EVKHFHLHDWQDFSIPGGPDVLVNFCH 152
F ++ T+ E H+ + L +T + V HF+ W D +P +NF
Sbjct: 145 RFGKFKITTTQVETHPHYVKSTLLLTDGTSATQTVTHFNFTAWPDHDVPKNTSEFLNFVL 204
Query: 153 LVR 155
VR
Sbjct: 205 EVR 207
>gnl|CDD|165109 PHA02742, PHA02742, protein tyrosine phosphatase; Provisional.
Length = 303
Score = 72.3 bits (177), Expect = 1e-15
Identities = 35/149 (23%), Positives = 63/149 (42%), Gaps = 14/149 (9%)
Query: 34 GFSNEAEYIAAQGPKADTVADFWTMVLQHQVVKIVMLCSFVEKGRVKCEKYFPDRVNEYF 93
G + + +I Q P +T DFW + Q QV IVM+ +E G+ C Y+
Sbjct: 88 GHNAKGRFICTQAPLEETALDFWQAIFQDQVRVIVMITKIMEDGKEACYPYWMPHERGKA 147
Query: 94 VFNNIRVGCTEQEVGSHHTCTHLRITRDS--EVLEVKHFHLHDWQDFSIPGGPDVLVNFC 151
++ + + ++ T+L +T + L++KHF DW +P P+ ++F
Sbjct: 148 THGEFKIKTKKIKSFRNYAVTNLCLTDTNTGASLDIKHFAYEDWPHGGLPRDPNKFLDFV 207
Query: 152 HLVRNSTPTSQLS------------VVHC 168
VR + + + +VHC
Sbjct: 208 LAVREADLKADVDIKGENIVKEPPILVHC 236
>gnl|CDD|227886 COG5599, PTP2, Protein tyrosine phosphatase [Signal transduction
mechanisms].
Length = 302
Score = 70.3 bits (172), Expect = 9e-15
Identities = 43/145 (29%), Positives = 64/145 (44%), Gaps = 30/145 (20%)
Query: 41 YIAAQGPKADTVADFWTMVLQHQVVK--IVMLCSFVEKGRVKCEKYFPDRVNE------- 91
YIA QGPK +T+ DFW MV + IVML S E R KC++Y+P ++
Sbjct: 94 YIATQGPKPETIDDFWKMVWHNVPNNGVIVMLTSLPEYNREKCDQYWPLGYDDTLIIGLR 153
Query: 92 ------YFVFNNIRVGCTEQEVGSHHTCTHLRITRDSEVLEVKHFHLHDWQDFSIPGGPD 145
Y +FN+ V E+ S + ++ HF +W DF+ PD
Sbjct: 154 VIKQKKYELFNDNIVNVHNFELTS----------INGPPKKIHHFQYINWVDFN---VPD 200
Query: 146 V--LVNFCHLVRNSTPTSQLSVVHC 168
+ L H + +S + +VHC
Sbjct: 201 IRSLTEVIHSLNDSPVRTGPIIVHC 225
>gnl|CDD|165114 PHA02747, PHA02747, protein tyrosine phosphatase; Provisional.
Length = 312
Score = 62.7 bits (152), Expect = 3e-12
Identities = 42/162 (25%), Positives = 68/162 (41%), Gaps = 14/162 (8%)
Query: 21 GPKADTVADFWTMGFSNEAEYIAAQGPKADTVADFWTMVLQHQVVKIVMLC-SFVEKGRV 79
G +D + W GF ++ ++IA QGP A+T ADFW V Q IVML + G
Sbjct: 75 GSTSDYIHANWIDGFEDDKKFIATQGPFAETCADFWKAVWQEHCSIIVMLTPTKGTNGEE 134
Query: 80 KCEKYFPDRVNEYFVFNNIRVGCTEQEVGSHHTCTHLRITRDS--EVLEVKHFHLHDWQD 137
KC +Y+ + + R+ + V + + T + IT + ++ HF +W +
Sbjct: 135 KCYQYWCLNEDGNIDMEDFRIETLKTSVRAKYILTLIEITDKILKDSRKISHFQCSEWFE 194
Query: 138 FSIPGGPDVLVNFCHLV--------RNSTPTSQL---SVVHC 168
P + F ++ + P L VVHC
Sbjct: 195 DETPSDHPDFIKFIKIIDINRKKSGKLFNPKDALLCPIVVHC 236
>gnl|CDD|165113 PHA02746, PHA02746, protein tyrosine phosphatase; Provisional.
Length = 323
Score = 58.5 bits (141), Expect = 1e-10
Identities = 40/148 (27%), Positives = 56/148 (37%), Gaps = 14/148 (9%)
Query: 34 GFSNEAEYIAAQGPKADTVADFWTMVLQHQVVKIVMLCSFVEKGRVKCEKYFPDRVNEYF 93
GF ++I AQGPK DT DF+ ++ +H+ IV L ++ KC + + +
Sbjct: 108 GFKEANKFICAQGPKEDTSEDFFKLISEHESQVIVSLTD-IDDDDEKCFELWTKEEDSEL 166
Query: 94 VFNNIRVGCTEQEVGSHHTCTHLRITRDSE--VLEVKHFHLHDWQDFSIPGGPDVLVNFC 151
F + T T L IT E+ HF DW D IP G +
Sbjct: 167 AFGRFVAKILDIIEELSFTKTRLMITDKISDTSREIHHFWFPDWPDNGIPTGMAEFLELI 226
Query: 152 HLVR-----------NSTPTSQLSVVHC 168
+ V N T VVHC
Sbjct: 227 NKVNEEQAELIKQADNDPQTLGPIVVHC 254
>gnl|CDD|214649 smart00404, PTPc_motif, Protein tyrosine phosphatase, catalytic
domain motif.
Length = 105
Score = 43.9 bits (104), Expect = 2e-06
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 126 EVKHFHLHDWQDFSIPGGPDVLVNFCHLVRNSTPTSQLS---VVHCRH 170
VKH+H W D +P PD ++ V+ + S+ S VVHC
Sbjct: 1 TVKHYHYTGWPDHGVPESPDSILELLRAVKKNLNQSESSGPVVVHCSA 48
>gnl|CDD|214469 smart00012, PTPc_DSPc, Protein tyrosine phosphatase, catalytic
domain, undefined specificity. Protein tyrosine
phosphatases. Homologues detected by this profile and
not by those of "PTPc" or "DSPc" are predicted to be
protein phosphatases with a similar fold to DSPs and
PTPs, yet with unpredicted specificities.
Length = 105
Score = 43.9 bits (104), Expect = 2e-06
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 126 EVKHFHLHDWQDFSIPGGPDVLVNFCHLVRNSTPTSQLS---VVHCRH 170
VKH+H W D +P PD ++ V+ + S+ S VVHC
Sbjct: 1 TVKHYHYTGWPDHGVPESPDSILELLRAVKKNLNQSESSGPVVVHCSA 48
>gnl|CDD|165107 PHA02740, PHA02740, protein tyrosine phosphatase; Provisional.
Length = 298
Score = 34.6 bits (79), Expect = 0.019
Identities = 22/119 (18%), Positives = 46/119 (38%), Gaps = 5/119 (4%)
Query: 34 GFSNEAEYIAAQGPKADTVADFWTMVLQHQVVKIVMLCSFVEKGRVKC-EKYFPDRVNEY 92
G+ E ++I D F + ++V IV++ +K KC +++ +
Sbjct: 86 GYDFEQKFICIINLCEDACDKFLQALSDNKVQIIVLISRHADK---KCFNQFWSLKEGCV 142
Query: 93 FVFNNIRVGCTEQEVGSHHTCTHLRIT-RDSEVLEVKHFHLHDWQDFSIPGGPDVLVNF 150
+ ++ E + H T L +T + + ++ HF W PD ++F
Sbjct: 143 ITSDKFQIETLEIIIKPHFNLTLLSLTDKFGQAQKISHFQYTAWPADGFSHDPDAFIDF 201
>gnl|CDD|187749 cd09291, Photo-RC_M, Subunit M of bacterial photosynthetic reaction
center. Bacterial photosynthetic reaction center (RC)
complex, subunit M. The bacterial photosynthetic
reaction center couples light-induced electron transfer
with pumping protons across the membrane using reactions
involving a quinone molecule (QB) that binds two
electrons and two protons at the active site. The
reaction center consists of three membrane-bound
subunits, designated L, M, and H, plus an additional
extracellular cytochrome subunit. The L and M subunits
are arranged around an axis of 2-fold rotational
symmetry perpendicular to the membrane, forming a
scaffold that maintains the cofactors in a precise
configuration. The L and M subunits have both sequence
and structural similarity, suggesting a common
evolutionary origin. The L and M subunits bind
noncovalently to the nine cofactors in 2-fold symmetric
branches: four bacteriochlorophylls (Bchl), two
bacteriopheophytins (Bphe), two ubiquinone molecules (QA
and QB), and a non-heme iron. Two Bchls on the
periplasmic side of the membrane form the 'special pair'
or dimer which is the primary electron donor for the
photosynthetic reactions. The electron transfer reaction
proceeds from the dimer to an intermediate acceptor
(PA), a primary quinone (QA), and a secondary quinone
(QB). Protons are translocated from the bacterial
cytoplasm to the periplasmic space, generating an
electrochemical gradient of protons (the protonmotive
force) that can be used to power reactions such as ATP
synthesis. The RC complex is found in photosynthetic
bacteria, such as purple bacteria and other
proteobacteria species.
Length = 297
Score = 31.6 bits (72), Expect = 0.19
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 6 SQWGFSNEAEYIAAQGPKADTVADF--WTMGFSNEAEYI 42
S++G E E I +G + F WTMGF+ E I
Sbjct: 216 SRFGGEREIEQITDRGTATERAQLFWRWTMGFNATMESI 254
>gnl|CDD|130185 TIGR01115, pufM, photosynthetic reaction center M subunit. This
model decribes the photosynthetic reaction center M
subunit in non-oxygenic photosynthetic bacteria.
Reaction center is an integral membrane pigment-protein
that carries out light-driven electron transfer
reactions. At the core of reacion center is a collection
light-harvesting cofactors and closely associated
polypeptides. The core protein complex is made of L, M
and H subunits. The common cofactors include
bacterichlorophyll, bacteriopheophytins, ubiquinone and
no-heme ferrous iron. The net result of electron tranfer
reactions is the establishment of proton electrochemical
gradient and production of reducing equivalents in form
of NADH. Ultimately the process results in the reduction
of C02 to carbohydrates(C6H12O6) In non-oxygenic
organisms, the electron donor is some organic acid and
not water. Much of our current functional understanding
of photosynthesis comes from the structural
determination, spectroscopic studies and mutational
analysis on the reaction center of Rhodobacter
sphaeroides [Energy metabolism, Electron transport,
Energy metabolism, Photosynthesis].
Length = 304
Score = 28.9 bits (65), Expect = 1.4
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 6 SQWGFSNEAEYIAAQGPKADTVADFW--TMGFSNEAEYI 42
S++G E E I +G A+ A FW TMGF+ E I
Sbjct: 226 SRFGGDRELEQITDRGTAAERAALFWRWTMGFNATMESI 264
>gnl|CDD|237736 PRK14504, PRK14504, photosynthetic reaction center subunit M;
Provisional.
Length = 315
Score = 28.1 bits (63), Expect = 2.2
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 6 SQWGFSNEAEYIAAQGPKADTVADFW--TMGFSNEAEYI 42
S++G E E I +G + A FW TMGF+ E I
Sbjct: 227 SRYGGEREIEQIVDRGTATERAALFWRWTMGFNATMESI 265
>gnl|CDD|130372 TIGR01305, GMP_reduct_1, guanosine monophosphate reductase,
eukaryotic. A deep split separates two families of GMP
reductase. This family includes both eukaryotic and some
proteobacterial sequences, while the other family
contains other bacterial sequences [Purines,
pyrimidines, nucleosides, and nucleotides, Nucleotide
and nucleoside interconversions].
Length = 343
Score = 26.4 bits (58), Expect = 8.0
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 128 KHFHLHDWQDFSIPGGPDVLVNFCHLVRNSTPTSQ 162
KH+ + +W+ F+ PD L N V S+ +S
Sbjct: 76 KHYSVDEWKAFATNSSPDCLQN----VAVSSGSSD 106
>gnl|CDD|238111 cd00187, TOP4c, DNA Topoisomerase, subtype IIA; domain A';
bacterial DNA topoisomerase IV (C subunit, ParC),
bacterial DNA gyrases (A subunit, GyrA),mammalian DNA
toposiomerases II. DNA topoisomerases are essential
enzymes that regulate the conformational changes in DNA
topology by catalysing the concerted breakage and
rejoining of DNA strands during normal cellular growth.
Length = 445
Score = 26.4 bits (59), Expect = 9.5
Identities = 6/26 (23%), Positives = 12/26 (46%), Gaps = 1/26 (3%)
Query: 18 AAQGPKADTVADFWTMGFSNE-AEYI 42
++ K + + +GFS A+ I
Sbjct: 369 SSDEAKKALIEELEKLGFSEIQADAI 394
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
0.324 0.136 0.441
Gapped
Lambda K H
0.267 0.0705 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,885,185
Number of extensions: 779828
Number of successful extensions: 848
Number of sequences better than 10.0: 1
Number of HSP's gapped: 836
Number of HSP's successfully gapped: 18
Length of query: 178
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 87
Effective length of database: 6,901,388
Effective search space: 600420756
Effective search space used: 600420756
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.4 bits)