RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5460
(994 letters)
>gnl|CDD|216263 pfam01044, Vinculin, Vinculin family.
Length = 850
Score = 632 bits (1632), Expect = 0.0
Identities = 267/463 (57%), Positives = 316/463 (68%), Gaps = 5/463 (1%)
Query: 1 METDIPILVLIEAARSGNEKEVEKAAENFADHANKLVEVANLACSMSNNEDGVKMVRYAA 60
++T P+ +LIEAA++G E+ E+ A+NF +HAN+LVEVA LACS SNN++ V+ +R AA
Sbjct: 376 LDTTTPLKLLIEAAKAGREENFEEKAQNFQEHANRLVEVARLACSCSNNKETVEAIRMAA 435
Query: 61 SSIASLYTQVINAARILAARPRSKVAQENMDVFKEAWDSQVRVLTEAVDDITTIDDFLAV 120
+ + SL QVINAARIL P SK AQENM+ FK W+ QVR LTEAVDDIT DDFLAV
Sbjct: 436 AQVESLTPQVINAARILLHNPGSKAAQENMETFKNQWEDQVRRLTEAVDDITDTDDFLAV 495
Query: 121 SENHILEDVNKCVLALQEGDADILDRTAGAIRGRSARVANVVAAEMDNYEPGIYTERVLE 180
SE HILEDVNKCV+A+Q D L TAG+I GR+ RV V AEMDN E +YTERV E
Sbjct: 496 SEEHILEDVNKCVMAIQNADPQTLVATAGSIAGRANRVLLVAKAEMDNSEDPVYTERVKE 555
Query: 181 AIKVLREQVMPNFATRVEVAVDALSTTPPKEVDEN--EFIDASRLVYDGVREIRRAVLMN 238
A+ +L + P FA EVAV+AL K +EN EF+DA RLVYD VR IR+AVLMN
Sbjct: 556 AVDILSNTIPPMFAEAKEVAVNALDPGAAKSWEENNYEFLDAVRLVYDAVRPIRQAVLMN 615
Query: 239 RTDEELDPEDIELDDQYTTSEAATMPRSKELGVDEYPDISGITTAREAMRKMTEEDKQKI 298
R+ EL P D E + A P T RE MR++ E+K KI
Sbjct: 616 RSPPEL-PTDSEFE--REDEPADPRPPPPVETEPPPRPPPPPETDREEMRRLPPEEKAKI 672
Query: 299 AQQVEFFRSEKLKFDREVAKWDDTGNDIIVLAKHMCMIMMEMTDFTRGRGPLKTTMDVIN 358
A QV+ F + K REVAKWD GNDII LAK MCMIMMEMTDFTRG+GPLKTTMDVIN
Sbjct: 673 AAQVQPFLAAAHKLHREVAKWDSKGNDIIALAKRMCMIMMEMTDFTRGKGPLKTTMDVIN 732
Query: 359 AAKKISEAGTNLDKLTRQIADQCPESSTKKDLLAYLQRIALYCHQLNITSKVKADVQNIS 418
AAKKI+EAG + +L RQIA QC +S K DLLAYL+RI LYC QL I SKVKA +
Sbjct: 733 AAKKIAEAGEEVTRLARQIARQCTDSRIKTDLLAYLERIPLYCTQLKILSKVKATMLGSG 792
Query: 419 GELIVSGLDSATSLIQAAKNLMNAVVLTVKSSYVASTKYPRQN 461
EL VSGLDSA SLIQ A+NLM +VV TVK++Y ASTK N
Sbjct: 793 NELSVSGLDSAESLIQNAQNLMQSVVQTVKAAYAASTKIRTDN 835
Score = 279 bits (715), Expect = 2e-80
Identities = 125/265 (47%), Positives = 143/265 (53%), Gaps = 73/265 (27%)
Query: 690 EAMRKMTEEDKQKIAQQVEFFRSEKLKFDREVAKWDDTGNDIIVLAKHMCMIMMEMTDFT 749
E MR++ E+K KIA QV+ F + K REVAKWD GNDII LAK MCMIMMEMTDFT
Sbjct: 659 EEMRRLPPEEKAKIAAQVQPFLAAAHKLHREVAKWDSKGNDIIALAKRMCMIMMEMTDFT 718
Query: 750 RGRGPLKTTMDVINAAKKISEAGTNLDKLTRQIADQCPESSTKKDLLAYLQRIALYCHQL 809
RG+GPLKTTMDVINAAKKI+EAG + +L RQIA QC +S K DLLAYL+RI LYC
Sbjct: 719 RGKGPLKTTMDVINAAKKIAEAGEEVTRLARQIARQCTDSRIKTDLLAYLERIPLYC--- 775
Query: 810 NITSKVKADVQKPTNKDLLAYLQRIALYCHQLNITSKVKADVQNISGELIVSGLDSATSL 869
QL I SKVKA + EL VSGLDSA SL
Sbjct: 776 -----------------------------TQLKILSKVKATMLGSGNELSVSGLDSAESL 806
Query: 870 IQAAKNLMNAVVLTVKSSYVASTKYPRQNQVALDSATSLIQAAKNLMNAVVLTVKSSYVA 929
IQ A+NLM +VV TVK++Y ASTK
Sbjct: 807 IQNAQNLMQSVVQTVKAAYAASTKI----------------------------------- 831
Query: 930 STKYPRQNQVASPIVVWKMKAPEKK 954
+ SP V WKMKAP K+
Sbjct: 832 ------RTDNNSPRVRWKMKAPWKQ 850
Score = 266 bits (682), Expect = 7e-76
Identities = 116/220 (52%), Positives = 144/220 (65%), Gaps = 20/220 (9%)
Query: 470 AIVDRILLVFSFMETDIPILVLIEAARSGNEKEVEKAAENFADHANKLVEVANLACSMSN 529
A+VD + SF++T P+ +LIEAA++G E+ E+ A+NF +HAN+LVEVA LACS SN
Sbjct: 366 AVVDHV--SDSFLDTTTPLKLLIEAAKAGREENFEEKAQNFQEHANRLVEVARLACSCSN 423
Query: 530 NEDGVKMVRYAASSIASLYTQVINAARILAARPRSKVAQENMDVFKEAWDSQSQVAQENM 589
N++ V+ +R AA+ + SL QVINAARIL P SK AQENM+ FK W+ Q
Sbjct: 424 NKETVEAIRMAAAQVESLTPQVINAARILLHNPGSKAAQENMETFKNQWEDQ-------- 475
Query: 590 DVFKEAWDSQVRVLTEAVDDITTIDDFLAVSENHILEDVNKCVLALQEGDADILDRTAGA 649
VR LTEAVDDIT DDFLAVSE HILEDVNKCV+A+Q D L TAG+
Sbjct: 476 ----------VRRLTEAVDDITDTDDFLAVSEEHILEDVNKCVMAIQNADPQTLVATAGS 525
Query: 650 IRGRSARVANVVAAEMDNYEPGIYTERVLEAIKVLREQGM 689
I GR+ RV V AEMDN E +YTERV EA+ +L
Sbjct: 526 IAGRANRVLLVAKAEMDNSEDPVYTERVKEAVDILSNTIP 565
>gnl|CDD|184699 PRK14478, PRK14478, nitrogenase molybdenum-cofactor biosynthesis
protein NifE; Provisional.
Length = 475
Score = 40.8 bits (96), Expect = 0.003
Identities = 25/86 (29%), Positives = 44/86 (51%), Gaps = 17/86 (19%)
Query: 633 LALQEGDADILDRTAGAIRGRSARVANVVAAEMDNYEPGIYTERVL---------EAIKV 683
L + DA++++RT I A+ A ++ Y P + +RVL +K
Sbjct: 287 LVERGADAELVERTEALIAEEEAK----AWAALEPYRPRLEGKRVLLYTGGVKSWSVVKA 342
Query: 684 LREQGME----AMRKMTEEDKQKIAQ 705
L+E GME +++K T+EDK++I +
Sbjct: 343 LQELGMEVVGTSVKKSTDEDKERIKE 368
>gnl|CDD|188126 TIGR01283, nifE, nitrogenase molybdenum-iron cofactor biosynthesis
protein NifE. This protein is part of the NifEN complex
involved in biosynthesis of the molybdenum-iron cofactor
used by the homologous NifDK complex of nitrogenase. In
a few species, the protein is found as a NifEN fusion
protein [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other, Central intermediary metabolism,
Nitrogen fixation].
Length = 453
Score = 36.2 bits (84), Expect = 0.084
Identities = 22/94 (23%), Positives = 41/94 (43%), Gaps = 19/94 (20%)
Query: 625 LEDVNKCVLALQE--GDADILDRTAGAIRGRSARVANVVAAEMDNYEPGIYTERVL---- 678
+ED +K + + + GD ++L RT I AR + ++ Y + ++
Sbjct: 276 IEDTSKALRDIADLFGDPELLKRTEELI----AREEAKIRPALEPYRERLKGKKAAIYTG 331
Query: 679 -----EAIKVLREQGMEAM----RKMTEEDKQKI 703
+ L++ GME + +K TEED +I
Sbjct: 332 GVKSWSVVSALQDLGMEVVATGTQKSTEEDYARI 365
>gnl|CDD|238930 cd01968, Nitrogenase_NifE_I, Nitrogenase_NifE_I: a subgroup of the
NifE subunit of the NifEN complex: NifE forms an
alpha2beta2 tetramer with NifN. NifE and NifN are
structurally homologous to nitrogenase MoFe protein
alpha and beta subunits respectively. NifEN
participates in the synthesis of the iron-molybdenum
cofactor (FeMoco) of the MoFe protein. NifB-co (an iron
and sulfur containing precursor of the FeMoco) from NifB
is transferred to the NifEN complex where it is further
processed to FeMoco. The NifEN bound precursor of FeMoco
has been identified as a molybdenum-free, iron- and
sulfur- containing analog of FeMoco. It has been
suggested that this NifEN bound precursor also acts as a
cofactor precursor in nitrogenase systems which require
a cofactor other than FeMoco: i.e. iron-vanadium
cofactor (FeVco) or iron only cofactor (FeFeco).
Length = 410
Score = 35.8 bits (83), Expect = 0.12
Identities = 21/94 (22%), Positives = 42/94 (44%), Gaps = 19/94 (20%)
Query: 625 LEDVNKCVLALQE--GDADILDRTAGAIRGRSARVANVVAAEMDNYEPGIYTERVL---- 678
+ D +K + + E GD ++++RT I AR + E+ Y + ++
Sbjct: 240 IRDTSKSLRNIAELLGDEELIERTEELIAREEAR----LRPELAPYRARLEGKKAALYTG 295
Query: 679 -----EAIKVLREQGMEAM----RKMTEEDKQKI 703
+ L++ GME + +K T+ED ++I
Sbjct: 296 GVKSWSLVSALQDLGMEVVATGTQKGTKEDYERI 329
>gnl|CDD|236177 PRK08186, PRK08186, allophanate hydrolase; Provisional.
Length = 600
Score = 32.9 bits (76), Expect = 0.99
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 8/54 (14%)
Query: 200 AVDALSTT--PPKEVDENEFIDASRLVYDG--VREIRRAV---LMNRTDEELDP 246
A+ L E+D + F++A+RL+Y+G V E R A + + +DP
Sbjct: 277 ALARLEALGAELVEIDFSPFLEAARLLYEGPWVAE-RYAAVGEFLEAHPDAVDP 329
>gnl|CDD|133138 cd05471, pepsin_like, Pepsin-like aspartic proteases, bilobal
enzymes that cleave bonds in peptides at acidic pH.
Pepsin-like aspartic proteases are found in mammals,
plants, fungi and bacteria. These well known and
extensively characterized enzymes include pepsins,
chymosin, renin, cathepsins, and fungal aspartic
proteases. Several have long been known to be medically
(renin, cathepsin D and E, pepsin) or commercially
(chymosin) important. Structurally, aspartic proteases
are bilobal enzymes, each lobe contributing a catalytic
Aspartate residue, with an extended active site cleft
localized between the two lobes of the molecule. The N-
and C-terminal domains, although structurally related by
a 2-fold axis, have only limited sequence homology
except the vicinity of the active site. This suggests
that the enzymes evolved by an ancient duplication
event. Most members of the pepsin family specifically
cleave bonds in peptides that are at least six residues
in length, with hydrophobic residues in both the P1 and
P1' positions. The active site is located at the groove
formed by the two lobes, with an extended loop
projecting over the cleft to form an 11-residue flap,
which encloses substrates and inhibitors in the active
site. Specificity is determined by nearest-neighbor
hydrophobic residues surrounding the catalytic
aspartates, and by three residues in the flap.The
enzymes are mostly secreted from cells as inactive
proenzymes that activate autocatalytically at acidic pH.
This family of aspartate proteases is classified by
MEROPS as the peptidase family A1 (pepsin A, clan AA).
Length = 283
Score = 32.4 bits (74), Expect = 0.99
Identities = 17/98 (17%), Positives = 37/98 (37%), Gaps = 16/98 (16%)
Query: 848 KADVQNISGELIVSGLDSA--------TSLIQAAKN----LMNAVVLTVKSSYVASTKYP 895
+ GEL G+D + T ++ ++ + + KS +S
Sbjct: 145 RDGDGGNGGELTFGGIDPSKYTGDLTYTPVVSNGPGYWQVPLDGISVGGKSVISSSGGG- 203
Query: 896 RQNQVALDSATSLIQAAKNLMNAVVLTVKSSYVASTKY 933
+DS TSLI ++ +A++ + ++ +S
Sbjct: 204 ---GAIVDSGTSLIYLPSSVYDAILKALGAAVSSSDGG 238
>gnl|CDD|225342 COG2721, UxaA, Altronate dehydratase [Carbohydrate transport and
metabolism].
Length = 381
Score = 32.2 bits (74), Expect = 1.4
Identities = 23/105 (21%), Positives = 40/105 (38%), Gaps = 31/105 (29%)
Query: 17 GNEKEVEKAAENFADHANKLVEVAN---------------LACSMSNNEDGV-------- 53
G KE+E E A ++++VAN L C S+ G+
Sbjct: 113 GTLKEIEAGIE----IAKEMLQVANADKREPTPLSELKVGLKCGGSDGFSGITANPALGK 168
Query: 54 ---KMVRYAASSIASLYTQVINAARILAARPRSK-VAQENMDVFK 94
K++R + I S +VI A +L R ++ V + + +
Sbjct: 169 ASDKLIRKGGTVILSETPEVIGAEHLLIKRAVNEEVHVKLVRSIR 213
Score = 32.2 bits (74), Expect = 1.4
Identities = 23/105 (21%), Positives = 40/105 (38%), Gaps = 31/105 (29%)
Query: 498 GNEKEVEKAAENFADHANKLVEVAN---------------LACSMSNNEDGV-------- 534
G KE+E E A ++++VAN L C S+ G+
Sbjct: 113 GTLKEIEAGIE----IAKEMLQVANADKREPTPLSELKVGLKCGGSDGFSGITANPALGK 168
Query: 535 ---KMVRYAASSIASLYTQVINAARILAARPRSK-VAQENMDVFK 575
K++R + I S +VI A +L R ++ V + + +
Sbjct: 169 ASDKLIRKGGTVILSETPEVIGAEHLLIKRAVNEEVHVKLVRSIR 213
>gnl|CDD|130130 TIGR01058, parE_Gpos, DNA topoisomerase IV, B subunit,
Gram-positive. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation step
of chromosome segregation. Not every bacterium has both
a topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 31.4 bits (71), Expect = 2.7
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 2/60 (3%)
Query: 675 ERVLEAIKVLREQGMEAMRKMTEEDKQKIAQQVEFFRSEKLKFDREVA-KWDDTGNDIIV 733
+R + E G+ E K + QV +F EK + EVA +++D ++ I+
Sbjct: 207 KRTNKTTVFFYENGLVDFVDYINETK-ETLSQVTYFEGEKNGIEVEVAFQFNDGDSENIL 265
>gnl|CDD|143457 cd07139, ALDH_AldA-Rv0768, Mycobacterium tuberculosis aldehyde
dehydrogenase AldA-like. The Mycobacterium
tuberculosis NAD+-dependent, aldehyde dehydrogenase PDB
structure, 3B4W, and the Mycobacterium tuberculosis
H37Rv aldehyde dehydrogenase AldA (locus Rv0768)
sequence, as well as the Rhodococcus rhodochrous ALDH
involved in haloalkane catabolism, and other similar
sequences, are included in this CD.
Length = 471
Score = 31.0 bits (71), Expect = 3.7
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 141 ADILDRTAGAIRGRSARVANVVAAEM 166
A +L R A A+ R+ +A + AE
Sbjct: 63 AAVLRRLADALEARADELARLWTAEN 88
Score = 31.0 bits (71), Expect = 3.7
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 640 ADILDRTAGAIRGRSARVANVVAAEM 665
A +L R A A+ R+ +A + AE
Sbjct: 63 AAVLRRLADALEARADELARLWTAEN 88
>gnl|CDD|222867 PHA02546, 47, endonuclease subunit; Provisional.
Length = 340
Score = 30.0 bits (68), Expect = 5.9
Identities = 18/71 (25%), Positives = 27/71 (38%), Gaps = 7/71 (9%)
Query: 792 KKDLLAYLQRIALYCHQLNITSKVKADVQKPTN----KDLLAYLQRIALYCHQLNITSKV 847
DL + + H L I KV + K L L Y +++IT +
Sbjct: 266 DDDLTKFESELEKVVHDLKIVEKVDDSSDVDDDEEEVKSTLTLLNE---YIDEIDITDED 322
Query: 848 KADVQNISGEL 858
K+ V+ I EL
Sbjct: 323 KSAVKAIMNEL 333
>gnl|CDD|226552 COG4066, COG4066, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 165
Score = 29.0 bits (65), Expect = 8.2
Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 7/77 (9%)
Query: 208 PPKEVDENEFIDA-SRLVYDGVREIRRAVLMNRTDEELDPEDIELDDQYTTSEAATMPRS 266
PP+ N +++A + + + + +IR+ + DEE D E ++
Sbjct: 37 PPRY--RNHYVEAMMKALIERINDIRKKSVDEIQDEEGDEEKLDEMLN-RIERFKKYYTP 93
Query: 267 KELGVDEYPDISGITTA 283
E + + +IS I
Sbjct: 94 DE---ERFINISKILCP 107
>gnl|CDD|133010 cd02517, CMP-KDO-Synthetase, CMP-KDO synthetase catalyzes the
activation of KDO which is an essential component of the
lipopolysaccharide. CMP-KDO Synthetase:
3-Deoxy-D-manno-octulosonate cytidylyltransferase
(CMP-KDO synthetase) catalyzes the conversion of CTP and
3-deoxy-D-manno-octulosonate into
CMP-3-deoxy-D-manno-octulosonate (CMP-KDO) and
pyrophosphate. KDO is an essential component of the
lipopolysaccharide found in the outer surface of
gram-negative eubacteria. It is also a constituent of
the capsular polysaccharides of some gram-negative
eubacteria. Its presence in the cell wall
polysaccharides of green algae and plant were also
discovered. However, they have not been found in yeast
and animals. The absence of the enzyme in mammalian
cells makes it an attractive target molecule for drug
design.
Length = 239
Score = 29.4 bits (67), Expect = 9.1
Identities = 19/78 (24%), Positives = 31/78 (39%), Gaps = 20/78 (25%)
Query: 473 DRILLVFSFMETDIPILV-------LIEAARSGNEKEVEKAAENFADHANKLVEVANLAC 525
DRI V ++ D I+V LI +++ D V++A LA
Sbjct: 77 DRIAEVAEKLDADDDIVVNVQGDEPLIPPE------MIDQVVAALKDDPG--VDMATLAT 128
Query: 526 SMSNNED-----GVKMVR 538
+S+ E+ VK+V
Sbjct: 129 PISDEEELFNPNVVKVVL 146
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 0.128 0.345
Gapped
Lambda K H
0.267 0.0754 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 48,709,716
Number of extensions: 4848113
Number of successful extensions: 6034
Number of sequences better than 10.0: 1
Number of HSP's gapped: 6024
Number of HSP's successfully gapped: 58
Length of query: 994
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 888
Effective length of database: 6,236,078
Effective search space: 5537637264
Effective search space used: 5537637264
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: 64 (28.4 bits)