RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16949
(232 letters)
>gnl|CDD|177879 PLN02235, PLN02235, ATP citrate (pro-S)-lyase.
Length = 423
Score = 208 bits (532), Expect = 1e-65
Identities = 95/223 (42%), Positives = 139/223 (62%), Gaps = 6/223 (2%)
Query: 11 DEEAYVCIYSSRNSDTILFHHQGGVDIGDVDAKALKLEIPVGQTGVTEEQVTSKLLINVA 70
D+E Y+ I S R +I F GG++I + K + +P +T E LI
Sbjct: 114 DQEFYLSIVSDRLGCSISFSECGGIEIEENWDKVKTIFLPTEAP-LTSEICAP--LIATL 170
Query: 71 PAK-KAMVAKFVTALYNMYVNLYFTYLEINPLVVTNDTIYILDLAAKLDSTADFICRAQW 129
P + + + +F+ ++ ++ +L FT+LE+NP + + Y LD+ +LD TA F +W
Sbjct: 171 PLEIRGKIEEFIKGVFAVFQDLDFTFLEMNPFTLVDGEPYPLDMRGELDDTAAFKNFKKW 230
Query: 130 GNIDYPPPFGRDAYPEEAYIADLDSKSGASLKLTILNKKGRIWTMVAGGGASVVYSDTIC 189
GNI++P PFGR P E++I LD K+ ASLK T+LN KGRIWTMVAGGGASV+Y+DT+
Sbjct: 231 GNIEFPLPFGRVMSPTESFIHGLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVG 290
Query: 190 DLGGASELANYGEYSGAPSEQQTYEYAKTILSLMTQEKHPQGK 232
DLG ASEL NY EYSGAP+E++ +YA+ ++ T +P G+
Sbjct: 291 DLGYASELGNYAEYSGAPNEEEVLQYARVVIDCAT--ANPDGR 331
>gnl|CDD|223123 COG0045, SucC, Succinyl-CoA synthetase, beta subunit [Energy
production and conversion].
Length = 387
Score = 109 bits (276), Expect = 2e-28
Identities = 58/220 (26%), Positives = 87/220 (39%), Gaps = 23/220 (10%)
Query: 10 QDEEAYVCIYSSRNSDTILF--HHQGGVDIGDVDAKALKLEIPVG---QTGVTEEQVTSK 64
+E Y+ I R+S + +GG+DI +V K + + V TG+ Q
Sbjct: 102 IKKEYYLSIVLDRSSRRPVLMASTEGGMDIEEVAEKTPEKIVKVSVDPLTGLRPYQAREL 161
Query: 65 LL-INVAPAKKAMVAKFVTALYNMYVNLYFTYLEINPLVVTND--TIYILDLAAKLDSTA 121
+ + VA + LY ++V T +EINPLVVT D + LD LD A
Sbjct: 162 AFKLGLEGELVKQVADIIKKLYKLFVEKDATLVEINPLVVTPDGGDVLALDAKITLDDNA 221
Query: 122 DFICRAQWGNIDYPPPFGRDAYPEEAYIADLDSKSGASLKLTILNKKGRIWTMVAGGGAS 181
F P + E SG L L+ G I +V G G +
Sbjct: 222 LF-----------RHPDLAELRDESEEDPREAEASGYGLNYVELD--GNIGCIVNGAGLA 268
Query: 182 VVYSDTICDLGGASELANYGEYSGAPSEQQTYEYAKTILS 221
+ D + GG + AN+ + G + ++ E K ILS
Sbjct: 269 MATMDIVKLYGG--KPANFLDVGGGATAERVKEAFKLILS 306
>gnl|CDD|234813 PRK00696, sucC, succinyl-CoA synthetase subunit beta; Provisional.
Length = 388
Score = 53.6 bits (130), Expect = 2e-08
Identities = 39/128 (30%), Positives = 56/128 (43%), Gaps = 27/128 (21%)
Query: 7 TFDQDEEAYVCIYSSRNSDTILFHHQGGVDIGDVDA----KALKLEI-PVGQTGVTEEQ- 60
D+ V + S+ +GG+DI +V K K+ I P+ TG+ Q
Sbjct: 113 VLDRATRRVVFMAST----------EGGMDIEEVAEETPEKIHKVAIDPL--TGLQPFQA 160
Query: 61 --VTSKLLINVAPAKKAMVAKFVTALYNMYVNLYFTYLEINPLVVTND-TIYILDLAAK- 116
+ KL + K+ AK + LY +V + +EINPLVVT D + LD AK
Sbjct: 161 REIAFKLGLPGEQVKQF--AKILMGLYKAFVEKDASLVEINPLVVTKDGDLIALD--AKI 216
Query: 117 -LDSTADF 123
D A F
Sbjct: 217 NFDDNALF 224
>gnl|CDD|233234 TIGR01016, sucCoAbeta, succinyl-CoA synthetase, beta subunit. This
model is designated subfamily because it does not
discriminate the ADP-forming enzyme ((EC 6.2.1.5) from
the GDP_forming (EC 6.2.1.4) enzyme. The N-terminal half
is described by the CoA-ligases model (pfam00549). The
C-terminal half is described by the ATP-grasp model
(pfam02222). This family contains a split seen both in a
maximum parsimony tree (which ignores gaps) and in the
gap pattern near position 85 of the seed alignment.
Eukaryotic and most bacterial sequences are longer and
contain a region similar to TXQTXXXG. Sequences from
Deinococcus radiodurans, Mycobacterium tuberculosis,
Streptomyces coelicolor, and the Archaea are 6 amino
acids shorter in that region and contain a motif
resembling [KR]G [Energy metabolism, TCA cycle].
Length = 386
Score = 48.5 bits (116), Expect = 9e-07
Identities = 63/225 (28%), Positives = 96/225 (42%), Gaps = 32/225 (14%)
Query: 9 DQDEEAYVCIYSSRNSD--TILFHHQGGVDIGDVDAKA----LKLEIPV--GQTGVTEEQ 60
D D+E Y+ I R++ I+ +GGVDI +V K+ +K I G +
Sbjct: 103 DIDKEYYLSIVIDRSARCPVIMASTEGGVDIEEVAEKSPEKIIKYAIDPLTGLLPYQARE 162
Query: 61 VTSKLLINVAPAKKAMVAKFVTALYNMYVNLYFTYLEINPLVVTND-TIYILDLAAKLDS 119
+ KL + K+ VA + LY +++ + +EINPLV+T D + LD +D
Sbjct: 163 IAKKLGLEGELVKQ--VADIIKKLYQIFLEYDASLVEINPLVITKDGNLIALDAKLTIDD 220
Query: 120 TADFICRAQWGNIDYPPPFGRDAYPEE---AYIADLDSKSGASLKLTILNKKGRIWTMVA 176
A F DY R+ ++ Y+A LD G I MV
Sbjct: 221 NALFRHPDLEEMRDYSQEDPREVLAKQWGLNYVA-LD---------------GNIGCMVN 264
Query: 177 GGGASVVYSDTICDLGGASELANYGEYSGAPSEQQTYEYAKTILS 221
G G ++ D I GG E AN+ + G S ++ E K +LS
Sbjct: 265 GAGLAMATMDIIKLYGG--EPANFLDVGGGASAERVREALKLVLS 307
>gnl|CDD|237594 PRK14046, PRK14046, malate--CoA ligase subunit beta; Provisional.
Length = 392
Score = 46.6 bits (111), Expect = 3e-06
Identities = 60/236 (25%), Positives = 99/236 (41%), Gaps = 39/236 (16%)
Query: 1 MYSEVSTFDQDEEAYVCIYSSRNSDTILF--HHQGGVDIGDVDAK---ALK---LEIPVG 52
+Y E + + E Y+ R S+ + +GG++I ++ AK A+ +E VG
Sbjct: 96 VYVETAD-PIERELYLGFVLDRKSERVRVIASARGGMEIEEIAAKEPEAIIQVVVEPAVG 154
Query: 53 QTGVTEEQVTSKLLINVAPAKKAMVAKFVTAL---YNMYVNLYFTYLEINPLVVT-NDTI 108
++ L +++ V++ V + Y + +L T LEINPLVVT +D +
Sbjct: 155 LQQFQAREIAFGLGLDIK-----QVSRAVKTIMGCYRAFRDLDATMLEINPLVVTKDDRV 209
Query: 109 YILDLAAKLDSTADFICRAQWGNIDYPPPFGRDAY---PEEAYIADLDSKSGASLKLTIL 165
LD D A F R + RD P EA A+ L+ +
Sbjct: 210 LALDAKMSFDDNALFR-RPNIAEM-------RDPSQEDPREAQAAEHG--------LSYV 253
Query: 166 NKKGRIWTMVAGGGASVVYSDTICDLGGASELANYGEYSGAPSEQQTYEYAKTILS 221
G I +V G G ++ D I GG E AN+ + G S ++ + + +LS
Sbjct: 254 GLDGDIGCIVNGAGLAMATMDMIKLAGG--EPANFLDVGGGASPERVAKAFRLVLS 307
>gnl|CDD|219843 pfam08442, ATP-grasp_2, ATP-grasp domain.
Length = 202
Score = 41.5 bits (98), Expect = 1e-04
Identities = 35/104 (33%), Positives = 48/104 (46%), Gaps = 12/104 (11%)
Query: 9 DQDEEAYVCIYSSRNSDTILF--HHQGGVDIGDVDAKA----LKLEIPVGQTGVTEEQ-- 60
D E Y+ I R S + +GGVDI +V AK K+ I TG+T Q
Sbjct: 102 DIAREYYLSIVLDRASRGPVLIASTEGGVDIEEVAAKNPEAIHKVPIDP-ATGLTPYQAR 160
Query: 61 -VTSKLLINVAPAKKAMVAKFVTALYNMYVNLYFTYLEINPLVV 103
+ KL + K+A A + LY ++V T +EINPLV
Sbjct: 161 EIAFKLGLEGELVKQA--ADIIKKLYKLFVERDATLVEINPLVE 202
>gnl|CDD|177736 PLN00124, PLN00124, succinyl-CoA ligase [GDP-forming] subunit beta;
Provisional.
Length = 422
Score = 42.0 bits (99), Expect = 1e-04
Identities = 64/220 (29%), Positives = 86/220 (39%), Gaps = 30/220 (13%)
Query: 13 EAYVCIYSSRNSD--TILFHHQGGVDIGDVDAK----ALKLEIPVGQTGVTEEQ---VTS 63
E Y I R S I+ +GG I D+ K +K+ I + G+T+E V
Sbjct: 142 EMYFAILLDRASAGPLIIACSKGGTSIEDLAEKFPEKIIKVPIDI-FKGITDEDAAKVVD 200
Query: 64 KLLINVAPAKKAMVAKFVTALYNMYVNLYFTYLEINPLVVTNDTIYIL-DLAAKLDSTAD 122
L VA A + V LY ++ T +EINPL T D + D D A
Sbjct: 201 GLAPKVADRNDA--IEQVKKLYKLFCKCDCTMVEINPLAETADGQLVAADAKLNFDDNAA 258
Query: 123 FICRAQWGNIDYPPPFG-RDAYPEEAYIADLDSKSGASLKLTILNKKGRIWTMVAGGGAS 181
F R + F RD E D + A L + G I MV G G +
Sbjct: 259 F--RQK-------EIFALRDTSQE-----DPREVAAAKADLNYIGLDGEIGCMVNGAGLA 304
Query: 182 VVYSDTICDLGGASELANYGEYSGAPSEQQTYEYAKTILS 221
+ D I GG+ AN+ + G SEQQ E K + S
Sbjct: 305 MATMDIIKLHGGSP--ANFLDVGGNASEQQVVEAFKILTS 342
>gnl|CDD|233889 TIGR02485, CobZ_N-term, precorrin 3B synthase CobZ. CobZ is
essential for cobalamin biosynthesis (by knockout of the
R. capsulatus gene ) and is complemented by the
characterized precorrin 3B synthase CobG. The enzyme has
been shown to contain flavin, heme and Fe-S cluster
cofactors and is believed to require dioxygen as a
substrate. This model identifies the N-terminal portion
of the R. capsulatus gene which, in other species exists
as a separate protein. The C-terminal portion is
homologous to the 2-component signal transduction system
protein CitB (TIGR02484) [Biosynthesis of cofactors,
prosthetic groups, and carriers, Heme, porphyrin, and
cobalamin].
Length = 432
Score = 30.2 bits (68), Expect = 0.94
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 133 DYPPPFGRDAYPEEAYIADLDSKSG 157
D P F RD+YP E + DL +G
Sbjct: 48 DIPTDFQRDSYPAEEFERDLAPVTG 72
>gnl|CDD|233077 TIGR00661, MJ1255, conserved hypothetical protein. This model
represents nearly the full length of MJ1255 from
Methanococcus jannaschii and of an unpublished protein
from Vibrio cholerae, as well as the C-terminal half of
a protein from Methanobacterium thermoautotrophicum. A
small region (~50 amino acids) within the domain appears
related to a family of sugar transferases [Hypothetical
proteins, Conserved].
Length = 321
Score = 29.1 bits (65), Expect = 1.9
Identities = 16/58 (27%), Positives = 21/58 (36%), Gaps = 1/58 (1%)
Query: 90 NLYFTYLEINPLVVTNDTIYILDLAAKLDSTADFICRAQWGNIDYPPPFGRDAYPEEA 147
E NP ++ +D Y +AAKL IC + YP YP A
Sbjct: 84 REINIIREYNPDLIISDFEYSTVVAAKLLKIP-VICISNQNYTRYPLKTDLIVYPTMA 140
>gnl|CDD|213346 cd12207, RasGAP_IQGAP3, Ras-GTPase Activating Domain of IQ motif
containing GTPase activating protein 3. This family
represents the IQ motif containing GTPase activating
protein 3 (IQGAP3), which associates with Ras
GTP-binding proteins. A primary function of IQGAP
proteins is to modulate cytoskeletal architecture. There
are three known IQGAP family members: IQGAP1, IQGAP2 and
IQGAP3. Human IQGAP1 and IQGAP2 share 62% identity.
IQGAPs are multi-domain molecules having a
calponin-homology (CH) domain which binds F-actin,
IQGAP-specific repeats, a single WW domain, four IQ
motifs that mediate interactions with calmodulin, and a
RasGAP related domain that binds active Rho family
GTPases. IQGAP is an essential regulator of cytoskeletal
function. IQGAP1 negatively regulates Ras family GTPases
by stimulating their intrinsic GTPase activity, the
protein actually lacks GAP activity. Both IQGAP1 and
IQGAP2 specifically bind to Cdc42 and Rac1, but not to
RhoA. Despite of their similarities to part of the
sequence of RasGAP, neither IQGAP1 nor IQGAP2 interacts
with Ras. IQGAP3, only present in mammals, regulates the
organization of the cytoskeleton under the regulation of
Rac1 and Cdc42 in neuronal cells. The depletion of
IQGAP3 is shown to impair neurite or axon outgrowth in
neuronal cells with disorganized cytoskeleton.
Length = 350
Score = 27.9 bits (62), Expect = 5.0
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 73 KKAMVAKFVTA----LYNMYVNL-YFTYLEINPLVVTNDTIYILDLAA 115
+ ++ KF A +Y + NL Y+ ++ NP VV D I+D +A
Sbjct: 166 RDSLQEKFPGASEDEVYKVVGNLLYYRFM--NPAVVAPDGFDIVDCSA 211
>gnl|CDD|180440 PRK06172, PRK06172, short chain dehydrogenase; Provisional.
Length = 253
Score = 27.0 bits (60), Expect = 7.1
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 3/71 (4%)
Query: 150 ADLDSKSGASLKLTILNKKGRIWTMVAGGGASVVYSDTICDLGGASELANYGEYSGAP-- 207
A+ D+ G ++K L K +I M+A GG ++V + ++ LG A +++ Y A
Sbjct: 107 AEFDAIMGVNVKGVWLCMKYQIPLMLAQGGGAIVNTASVAGLGAAPKMSIYAASKHAVIG 166
Query: 208 -SEQQTYEYAK 217
++ EYAK
Sbjct: 167 LTKSAAIEYAK 177
>gnl|CDD|173607 PTZ00417, PTZ00417, lysine-tRNA ligase; Provisional.
Length = 585
Score = 27.3 bits (60), Expect = 7.3
Identities = 31/105 (29%), Positives = 42/105 (40%), Gaps = 15/105 (14%)
Query: 97 EINP-LVVTNDTIYILDLAAKLDSTADFICRAQWGNIDYPPPFGRDAYPEEAYIADLDSK 155
E++P L N + +I + AK G YP F R E D
Sbjct: 79 EVDPRLYYENRSKFIQEQKAK-------------GINPYPHKFERTITVPEFVEKYQDLA 125
Query: 156 SGASLKLTILNKKGRIWTMVAGGGASVVYSDTICDLGGASELANY 200
SG L+ TILN GRI V+ G + + D + D LAN+
Sbjct: 126 SGEHLEDTILNVTGRI-MRVSASGQKLRFFDLVGDGAKIQVLANF 169
>gnl|CDD|217208 pfam02734, Dak2, DAK2 domain. This domain is the predicted
phosphatase domain of the dihydroxyacetone kinase
family.
Length = 174
Score = 26.7 bits (60), Expect = 8.9
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 1/40 (2%)
Query: 146 EAYIADLDSKSGASLKLTILNKKGRIWTMVAGGGASVVYS 185
EA + LD+ A + +L AGG + +Y
Sbjct: 16 EAVLKALDALEDADIG-EVLKAIAMALLSGAGGTSGPLYG 54
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
0.315 0.133 0.385
Gapped
Lambda K H
0.267 0.0868 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,549,312
Number of extensions: 1070377
Number of successful extensions: 772
Number of sequences better than 10.0: 1
Number of HSP's gapped: 766
Number of HSP's successfully gapped: 21
Length of query: 232
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 138
Effective length of database: 6,768,326
Effective search space: 934028988
Effective search space used: 934028988
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.5 bits)