RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12854
(265 letters)
>gnl|CDD|189012 cd09605, M3A, Peptidase M3A family includes Thimet oligopeptidase,
dipeptidyl carboxypeptidase and mitochondrial
intermediate peptidase. The peptidase M3-like family,
also called neurolysin-like family, is part of the
"zincins" metallopeptidases, and includes M3, M2 and M32
families of metallopeptidases. The M3 family is
subdivided into two subfamilies: the widespread M3A,
which comprises a number of high-molecular mass endo-
and exopeptidases from bacteria, archaea, protozoa,
fungi, plants and animals, and the small M3B, whose
members are enzymes primarily from bacteria. Well-known
mammalian/eukaryotic M3A endopeptidases are the thimet
oligopeptidase (TOP; endopeptidase 3.4.24.15),
neurolysin (alias endopeptidase 3.4.24.16), and the
mitochondrial intermediate peptidase. The first two are
intracellular oligopeptidases, which act only on
relatively short substrates of less than 20 amino acid
residues, while the latter cleaves N-terminal
octapeptides from proteins during their import into the
mitochondria. The M3A subfamily also contains several
bacterial endopeptidases, collectively called
oligopeptidases A, as well as a large number of
bacterial carboxypeptidases, called dipeptidyl
peptidases (Dcp; Dcp II; peptidyl dipeptidase; EC
3.4.15.5). The peptidases in the M3 family contain the
HEXXH motif that forms the active site in conjunction
with a C-terminally-located Glutamic acid (Glu) residue.
A single zinc ion is ligated by the side-chains of the
two Histidine (His) residues, and the more C-terminal
Glu. Most of the peptidases are synthesized without
signal peptides or propeptides, and function
intracellularly. The structure of neurolysin shows
similarities to those of angiotensin-converting enzyme
(ACE; peptidyl-dipeptidase A) peptidase unit 2 belonging
to peptidase family M2. ACE is an enzyme responsible for
cleavage of dipeptides from the C-termini of proteins,
notably converting angiotensin I to angiotensin II in
mammals. There are similarities to the thermostable
carboxypeptidases from Pyrococcus furiosus
carboxypeptidase (PfuCP), and Thermus aquaticus (TaqCP),
belonging to peptidase family M32. Little is known about
function of this family, including carboxypeptidases Taq
and Pfu.
Length = 590
Score = 155 bits (394), Expect = 1e-43
Identities = 81/264 (30%), Positives = 114/264 (43%), Gaps = 39/264 (14%)
Query: 8 TVITPLNTLILNLTEPQYGKPCLLTFKQVENLFFHFGSLLQRSLTATHYSDVSGVNNVEW 67
+ P+ L+ N T+P GKP LLT +VE LF FG L L+ T Y +SG VE
Sbjct: 351 SRQLPVAALVCNFTKPTGGKPALLTHDEVETLFHEFGHALHGLLSRTKYPSLSG-TRVER 409
Query: 68 D-----SVYIINYFLTHFLYEERVFAELNSHFATGEKLKMTDEQLKALRAH---NAGIDV 119
D S + ++ ++ V H+ TGE + DE ++ L A N G+
Sbjct: 410 DFVELPSQ-----LMENWAWDPEVLKLFARHYETGEP--LPDELVEKLIAARNFNQGLAT 462
Query: 120 CSELFKANLDLQLHNGPKPHWSEIS----RELYPLHFGFPIDKYSNLPCRFVEVGSGDLA 175
+L A LDL LH+ P + L P + F + G A
Sbjct: 463 LRQLAFALLDLALHSLDPPEDGDDVTFELAALREEGLPVPPVPGTYFQASFGHLFGGGYA 522
Query: 176 AGYYSFLWSKLVSADIFYAFKEDGEGRLEDESGRSDSGVSGGERTEPNVGSRLRDTFLTF 235
AGYYS+LW+++++AD F AF E G + G R RD L+
Sbjct: 523 AGYYSYLWAEVLAADAFSAFFEAG--------PLN-----------RETGERFRDEILSP 563
Query: 236 GGSCHSSEVFRRFRGRDPCFKPFL 259
GGS E+FR F GR+P + L
Sbjct: 564 GGSKDPMELFRDFLGREPSIEALL 587
>gnl|CDD|216500 pfam01432, Peptidase_M3, Peptidase family M3. This is the Thimet
oligopeptidase family, large family of mammalian and
bacterial oligopeptidases that cleave medium sized
peptides. The group also contains mitochondrial
intermediate peptidase which is encoded by nuclear DNA
but functions within the mitochondria to remove the
leader sequence.
Length = 450
Score = 145 bits (368), Expect = 8e-41
Identities = 76/255 (29%), Positives = 109/255 (42%), Gaps = 26/255 (10%)
Query: 16 LILNLTEPQYGKPCLLTFKQVENLFFHFGSLLQRSLTATHYSDVSGVNNVEWDSVYIINY 75
L+ N T+P GKP LLT VE LF FG + L+ T YS VSG N V D I +
Sbjct: 216 LLCNFTKPSSGKPSLLTHDDVETLFHEFGHSMHSLLSRTEYSYVSGTN-VPIDFAEIPSQ 274
Query: 76 FLTHFLYEERVFAELNSHFATGEKLKMTD-EQLKALRAHNAGIDVCSELFKANLDLQLH- 133
F ++L+E + L+ H+ TGE + E+L + NAG+ + +L A D ++H
Sbjct: 275 FNENWLWEPLLLNLLSRHYETGEPIPAELLEKLIKSKNVNAGLFLFRQLMFAAFDQEIHE 334
Query: 134 ----NGPKPHWSEISRELYPLHFGFPIDKYSNLPCRFVEVGSGDLAAGYYSFLWSKLVSA 189
+ E EL ++G P+ P F + AA YYS+L++ ++
Sbjct: 335 AAEEDQKLDFLLEEYAELNKKYYGDPVTPDEASPLSFSHIFPHGYAANYYSYLYATGLAL 394
Query: 190 DIFYAFKEDGEGRLEDESGRSDSGVSGGERTEPNVGSRLRDTFLTFGGSCHSSEVFRRFR 249
DIF F E G R FL+ GGS E+ ++F
Sbjct: 395 DIFEKFFEQDP-------------------LNRETGLRYYLEFLSRGGSLDPLELLKKFG 435
Query: 250 GRDPCFKPFLDMFRL 264
GR P L L
Sbjct: 436 GRMPSADALLRALGL 450
>gnl|CDD|223416 COG0339, Dcp, Zn-dependent oligopeptidases [Amino acid transport
and metabolism].
Length = 683
Score = 141 bits (358), Expect = 2e-38
Identities = 84/263 (31%), Positives = 125/263 (47%), Gaps = 35/263 (13%)
Query: 7 KTVITPLNTLILNLTEPQYGKPCLLTFKQVENLFFHFGSLLQRSLTATHYSDVSGVNNVE 66
P+ L+ N T+P GKP LL+ +V LF FG L LT Y VSG NV
Sbjct: 439 GGGQKPVIYLVCNFTKPVGGKPALLSHDEVTTLFHEFGHGLHHLLTRVKYPGVSGT-NVP 497
Query: 67 WDSVYIINYFLTHFLYEERVFAELNSHFATGEKL--KMTDEQLKALRAHNAGIDVCSELF 124
WD V + + F+ ++ +E V A+ H+ TGE L ++ D+ L A + AG+ +L
Sbjct: 498 WDFVELPSQFMENWCWEPEVLAKYARHYQTGEPLPKELLDKMLAA-KNFQAGLFTLRQLE 556
Query: 125 KANLDLQLHNGPKPH--------WSEISRELYPLHFGFPIDKYSNLPCRFVEVGSGDLAA 176
A D++LH P +E+ +++ L P P F + +G +A
Sbjct: 557 FALFDMRLHTEFDPDANADILEFEAEVLKKVAVL----PSIPPRRRPHSFGHIFAGGYSA 612
Query: 177 GYYSFLWSKLVSADIFYAFKEDGEGRLEDESGRSDSGVSGGERTEPNVGSRLRDTFLTFG 236
GYYS+LW++++SAD F AF+E+G + G R RD L+ G
Sbjct: 613 GYYSYLWAEVLSADAFAAFEEEG-------------PFN------RETGQRFRDAILSRG 653
Query: 237 GSCHSSEVFRRFRGRDPCFKPFL 259
GS E+F+ FRGR+P L
Sbjct: 654 GSRDPMELFKAFRGREPSIDALL 676
>gnl|CDD|188995 cd06456, M3A_DCP, Peptidase family M3 dipeptidyl carboxypeptidase
(DCP). Peptidase family M3 dipeptidyl carboxypeptidase
(DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This
metal-binding M3A family also includes oligopeptidase A
(OpdA; EC 3.4.24.70) enzyme. DCP cleaves dipeptides off
the C-termini of various peptides and proteins, the
smallest substrate being N-blocked tripeptides and
unblocked tetrapeptides. DCP from E. coli is inhibited
by the anti-hypertensive drug captopril, an inhibitor of
the mammalian angiotensin converting enzyme (ACE, also
called peptidyl dipeptidase A). Oligopeptidase A (OpdA)
may play a specific role in the degradation of signal
peptides after they are released from precursor forms of
secreted proteins. It can also cleave N-acetyl-L-Ala.
Length = 654
Score = 132 bits (334), Expect = 4e-35
Identities = 80/259 (30%), Positives = 111/259 (42%), Gaps = 29/259 (11%)
Query: 8 TVITPLNTLILNLTEPQYGKPCLLTFKQVENLFFHFGSLLQRSLTATHYSDVSGVNNVEW 67
P+ + N T+P GKP LLT +V LF FG L L+ Y +SG NV W
Sbjct: 413 GGQLPVAYNVCNFTKPAGGKPALLTHDEVTTLFHEFGHALHGLLSDVDYPSLSGT-NVVW 471
Query: 68 DSVYIINYFLTHFLYEERVFAELNSHFATGEKLKMTDEQLKALRA---HNAGIDVCSELF 124
D V + + F+ ++ +E V A H+ TGE + DE + L A N G +L
Sbjct: 472 DFVELPSQFMENWAWEPEVLALYARHYETGE--PLPDELIDKLLAARNFNQGFATVRQLA 529
Query: 125 KANLDLQLH----NGPKPHWSEISRELYPLHFGFPIDKYSNLPCRFVEVGSGDLAAGYYS 180
A LD+ LH + L P F + +G AAGYYS
Sbjct: 530 FALLDMALHSLYDPEAGDVVAFELEALREEGLVPPPIPPRYRSTYFSHIFAGGYAAGYYS 589
Query: 181 FLWSKLVSADIFYAFKEDGEGRLEDESGRSDSGVSGGERTEPNVGSRLRDTFLTFGGSCH 240
+ W++++ AD F AF+E G + + G R RD L+ GGS
Sbjct: 590 YKWAEVLDADAFEAFEEAG---IFN----------------RETGKRFRDEILSRGGSRD 630
Query: 241 SSEVFRRFRGRDPCFKPFL 259
E+FR FRGR+P L
Sbjct: 631 PMELFRAFRGREPDIDALL 649
>gnl|CDD|188994 cd06455, M3A_TOP, Peptidase M3 Thimet oligopeptidase (TOP) also
includes neurolysin. Peptidase M3 Thimet oligopeptidase
(TOP; PZ-peptidase; endo-oligopeptidase A; endopeptidase
24.15; soluble metallo-endopeptidase; EC 3.4.24.15)
family also includes neurolysin (endopeptidase 24.16,
microsomal endopeptidase, mitochondrial oligopeptidase
M, neurotensin endopeptidase, soluble angiotensin
II-binding protein, thimet oligopeptidase II) which
hydrolyzes oligopeptides such as neurotensin, bradykinin
and dynorphin A. TOP and neurolysin are neuropeptidases
expressed abundantly in the testis, but also found in
the liver, lung and kidney. They are involved in the
metabolism of neuropeptides under 20 amino acid residues
long and cleave most bioactive peptides at the same
sites, but recognize different positions on some
naturally occurring and synthetic peptides; they cleave
at distinct sites on the 13-residue bioactive peptide
neurotensin, which modulates central dopaminergic and
cholinergic circuits. TOP has been shown to degrade
peptides released by the proteasome, limiting the extent
of antigen presentation by major histocompatibility
complex class I molecules, and has been associated with
amyloid protein precursor processing.
Length = 637
Score = 122 bits (309), Expect = 9e-32
Identities = 79/261 (30%), Positives = 120/261 (45%), Gaps = 44/261 (16%)
Query: 12 PLNTLILNLTEPQYGKPCLLTFKQVENLFFHFGSLLQRSLTATHYSDVSGVNNVEWDSVY 71
P+ L+ N +P KP LL +VE F FG ++ L T Y+ SG VE D V
Sbjct: 405 PVAALVCNFPKPTADKPSLLKHDEVETFFHEFGHVMHHLLGRTKYARFSGTR-VERDFVE 463
Query: 72 IINYFLTHFLYEERVFAELNSHFATGEKLKMTDEQLKALRAH---NAGIDVCSELFKANL 128
+ L ++ +E V L+ H+ TGE + DE ++ L A N G+ +LF A
Sbjct: 464 APSQMLENWCWEPEVLKRLSKHYKTGEPI--PDELIERLIASRHVNRGLFTLRQLFFALF 521
Query: 129 DLQLHNGPKPH------WSEISRELYPLHFGFPIDKYSNLPCRFVEVGSGDLA----AGY 178
DL +H ++++ E+ P + ++ F G LA AGY
Sbjct: 522 DLAIHTRDPAELDTTKLYNDLREEISL----IPAVEGTHFYASF-----GHLAGGYDAGY 572
Query: 179 YSFLWSKLVSADIFYAFKEDGEGRLEDESGRSDSGVSGGERTEPNVGSRLRDTFLTFGGS 238
Y +LWS++ +AD+FY+F +DG + P VG R RDT L GGS
Sbjct: 573 YGYLWSEVFAADMFYSFFKDG--------PLN-----------PEVGRRYRDTILAPGGS 613
Query: 239 CHSSEVFRRFRGRDPCFKPFL 259
++++ + F GR+P FL
Sbjct: 614 KDAADMLKNFLGREPNNDAFL 634
>gnl|CDD|182832 PRK10911, PRK10911, oligopeptidase A; Provisional.
Length = 680
Score = 117 bits (296), Expect = 5e-30
Identities = 78/248 (31%), Positives = 118/248 (47%), Gaps = 26/248 (10%)
Query: 12 PLNTLILNLTEPQYGKPCLLTFKQVENLFFHFGSLLQRSLTATHYSDVSGVNNVEWDSVY 71
P+ L N P GKP L T +V LF FG L LT + VSG++ V WD+V
Sbjct: 440 PVAYLTCNFNRPVNGKPALFTHDEVITLFHEFGHGLHHMLTRIETAGVSGISGVPWDAVE 499
Query: 72 IINYFLTHFLYEERVFAELNSHFATGEKL--KMTDEQLKALRAHNAGIDVCSELFKANLD 129
+ + F+ ++ +E A ++ H+ TGE L ++ D+ L A + + A + + +L D
Sbjct: 500 LPSQFMENWCWEPEALAFISGHYETGEPLPKELLDKMLAA-KNYQAALFILRQLEFGLFD 558
Query: 130 LQLHNGPKPHWS----EISRELYPLHFGFPIDKYSNLPCRFVEVGSGDLAAGYYSFLWSK 185
+LH P E E+ P + P F + +G AAGYYS+LW+
Sbjct: 559 FRLHAEFDPDQGAKILETLAEIKKQVAVVPSPSWGRFPHAFSHIFAGGYAAGYYSYLWAD 618
Query: 186 LVSADIFYAFKEDGEGRLEDESGRSDSGVSGGERTEPNVGSRLRDTFLTFGGSCHSSEVF 245
+++AD F F+E EG E+G+S D L+ GGS E+F
Sbjct: 619 VLAADAFSRFEE--EGIFNRETGQS-----------------FLDNILSRGGSEEPMELF 659
Query: 246 RRFRGRDP 253
+RFRGR+P
Sbjct: 660 KRFRGREP 667
>gnl|CDD|188996 cd06457, M3A_MIP, Peptidase M3 mitochondrial intermediate peptidase
(MIP). Peptidase M3 mitochondrial intermediate
peptidase (MIP; EC 3.4.24.59) belongs to the widespread
subfamily M3A, that show similarity to the Thimet
oligopeptidase (TOP). It is one of three peptidases
responsible for the proteolytic processing of both,
nuclear and mitochondrial encoded precursor polypeptides
targeted to the various subcompartments of the
mitochondria. It cleaves intermediate-size proteins
initially processed by mitochondrial processing
peptidase (MPP) to yield a processing intermediate with
a typical N-terminal octapeptide that is sequentially
cleaved by MIP to mature-size protein. MIP cleaves
precursor proteins of respiratory components, including
subunits of the electron transport chain and
tri-carboxylic acid cycle enzymes, and components of the
mitochondrial genetic machinery, including ribosomal
proteins, translation factors, and proteins required for
mitochondrial DNA metabolism. It has been suggested that
the human MIP (HMIP polypeptide; gene symbol MIPEP) may
be one of the loci predicted to influence the clinical
manifestations of Friedreich's ataxia (FRDA), an
autosomal recessive neurodegenerative disease caused by
lack of human frataxin. These proteins are enriched in
cysteine residues, two of which are highly conserved,
suggesting their importance to stability as well as in
formation of metal binding sites, thus playing a role in
MIP activity.
Length = 606
Score = 83.8 bits (208), Expect = 2e-18
Identities = 65/258 (25%), Positives = 103/258 (39%), Gaps = 49/258 (18%)
Query: 12 PLNTLILNLTEPQYGKPCLLTFKQVENLFFHFG----SLLQRSLTATHYSDVSG----VN 63
P+ L+ N P P LL+ +VE LF G S+L R T Y VSG +
Sbjct: 373 PVVALVCNFPPPSGSSPTLLSHGEVETLFHEMGHAMHSMLGR----TKYQHVSGTRCATD 428
Query: 64 NVEWDSVYIINYFLTHFLYEERVFAELNSHFATGEKLKMTDEQLKALRAHN---AGIDVC 120
VE S+ + +F ++ RV + H++TGE + ++ + L A A ++
Sbjct: 429 FVELPSI-----LMEYFAWDPRVLSLFARHYSTGE--PLPEKLVARLCASKFLFAALETQ 481
Query: 121 SELFKANLDLQLHNG-PKPHW---SEISRELYPLHFGFPIDKYSNLPCRFVE-VGSGDLA 175
++ A LD + H+ P P ++I +L + G P + RF VG G
Sbjct: 482 QQILYALLDQEYHSEHPLPPSFSSTDIYHDLQRKYSGLPYVPGTAWQLRFGHLVGYG--- 538
Query: 176 AGYYSFLWSKLVSADIFYAFKEDGEGRLEDESGRSDSGVSGGERTEPNVGSRLRDTFLTF 235
A YYS+L+ + +++ I+ E G RLR+ L
Sbjct: 539 ATYYSYLFDRAIASKIWQKLFAADPLSRE-------------------AGERLREEVLKH 579
Query: 236 GGSCHSSEVFRRFRGRDP 253
GG E+ G P
Sbjct: 580 GGGKDPWELLADVLGEPP 597
>gnl|CDD|182353 PRK10280, PRK10280, dipeptidyl carboxypeptidase II; Provisional.
Length = 681
Score = 80.6 bits (199), Expect = 3e-17
Identities = 77/277 (27%), Positives = 111/277 (40%), Gaps = 58/277 (20%)
Query: 3 IFGTKTVITPLNTLILNLTEPQYGKPCLLTFKQVENLFFHFGSLLQRSLTATHYSDVSGV 62
+ T+ VI + N +P G+P LL + V LF FG L Y+ +SG
Sbjct: 436 LNETRPVIYN----VCNYQKPAAGQPALLLWDDVITLFHEFGHTLHGLFARQRYATLSGT 491
Query: 63 NN----VEWDSVYIINYFLTHFLYEERVFAELNSHFATGEKLKMTDE-QLKALRAH--NA 115
N VE+ S IN H+ +VFA H+ +GE M DE Q K A N
Sbjct: 492 NTPRDFVEFPSQ--IN---EHWASHPQVFARYARHYQSGEA--MPDELQEKMRNASLFNK 544
Query: 116 GIDVCSELFKANLDLQLHNGPKPHWSEISRELYPLH---FGFPIDKYSNL-----PCR-- 165
G D+ L A LD+ W + F NL P R
Sbjct: 545 GYDMSELLSAALLDM--------RWHCLEENEAMQDVDDFELRALVAENLDLPAVPPRYR 596
Query: 166 ---FVEVGSGDLAAGYYSFLWSKLVSADIFYAFKEDGEGRLEDESGRSDSGVSGGERTEP 222
F + G AAGYY++LW+++++ D + F E +G L E+G+
Sbjct: 597 SSYFAHIFGGGYAAGYYAYLWTQMLADDGYQWFVE--QGGLTRENGQ------------- 641
Query: 223 NVGSRLRDTFLTFGGSCHSSEVFRRFRGRDPCFKPFL 259
R R+ L+ G S ++R++RG P P L
Sbjct: 642 ----RFREAILSRGNSTDLERLYRQWRGHAPQIMPML 674
>gnl|CDD|188993 cd06258, M3_like, Peptidase M3-like family, a zincin
metallopeptidase, includes M3 and M32 families. The
peptidase M3-like family, also called neurolysin-like
family, is part of the "zincins" metallopeptidases, and
includes M3 and M32 families of metallopeptidases. The
M3 family is subdivided into two subfamilies: the
widespread M3A, which comprises a number of
high-molecular mass endo- and exopeptidases from
bacteria, archaea, protozoa, fungi, plants and animals,
and the small M3B, whose members are enzymes primarily
from bacteria. Well-known mammalian/eukaryotic M3A
endopeptidases are the thimet oligopeptidase (TOP;
endopeptidase 3.4.24.15), neurolysin (alias
endopeptidase 3.4.24.16), and the mitochondrial
intermediate peptidase. The first two are intracellular
oligopeptidases, which act only on relatively short
substrates of less than 20 amino acid residues, while
the latter cleaves N-terminal octapeptides from proteins
during their import into the mitochondria. The M3A
subfamily also contains several bacterial
endopeptidases, collectively called oligopeptidases A,
as well as a large number of bacterial
carboxypeptidases, called dipeptidyl peptidases (Dcp;
Dcp II; peptidyl dipeptidase; EC 3.4.15.5). The
peptidases in the M3 family contain the HEXXH motif that
forms the active site in conjunction with a
C-terminally-located Glutamic acid (Glu) residue. A
single zinc ion is ligated by the side-chains of the two
Histidine (His) residues, and the more C-terminal Glu.
Most of the peptidases are synthesized without signal
peptides or propeptides, and function intracellularly.
There are similarities to the thermostable
carboxypeptidases from Pyrococcus furiosus
carboxypeptidase (PfuCP), and Thermus aquaticus (TaqCP),
belonging to peptidase family M32. Little is known about
function of this family, including carboxypeptidases Taq
and Pfu.
Length = 400
Score = 38.5 bits (90), Expect = 0.003
Identities = 32/205 (15%), Positives = 60/205 (29%), Gaps = 40/205 (19%)
Query: 75 YFLTHFLYEERVFAELNSHFAT--------GEKLKMTDEQLKALRAHNAGIDVCSE---L 123
T E + K ++ K +RAH + L
Sbjct: 219 RAPTSLATTE-AQSMFFERLTEDPEWLKRYLGVPKGNEDPDKTIRAHLRASALYLLRRIL 277
Query: 124 FKANLDLQLHNGPKPH-----WSEISRELYPLHFGFPIDKYSNLPCRFVEVGSGDLAAGY 178
+ L+ P W +++REL + P + + + Y
Sbjct: 278 AVLYFEKALYENPDQELLAELWWKLARELLGVR---PEGPSPPPWAAKIHI---ASSPVY 331
Query: 179 Y-SFLWSKLVSADIFYAFKEDGEGRLEDESGRSDSGVSGGERTEPNVGSRLRDTFLTFGG 237
Y +L +++++A + KE G L D P G+ L++ G
Sbjct: 332 YHGYLLAEMLAAQLRAHLKEK-FGDLVDN---------------PEAGAWLKEKLWRPGN 375
Query: 238 SCHSSEVFRRFRGRDPCFKPFLDMF 262
S E+ + G + F+
Sbjct: 376 SLDWEELLKSATGEPLNAEYFVAQL 400
>gnl|CDD|200106 TIGR01456, CECR5, HAD-superfamily class IIA hydrolase, TIGR01456,
CECR5. This hypothetical equivalog is a member of the
Class IIA subfamily of the haloacid dehalogenase
superfamily of aspartate-nucleophile hydrolases. The
sequences modelled by this equivalog are all eukaryotes.
One sequence (GP|13344995) is called "Cat Eye Syndrome
critical region protein 5" (CECR5). This gene has been
cloned from a pericentromere region of human chromosome
22 believed to be the location of the gene or genes
responsible for Cat Eye Syndrome. This is one of a
number of candidate genes. The Schizosaccharomyces pombe
sequence (EGAD|138276) is annotated as "phosphatidyl
synthase," however this is due entirely to a C-terminal
region of the protein (outside the region of similarity
of This model) which is highly homologous to a family of
CDP-alcohol phosphatidyltransferases. (Thus, the
annotation of GP|4226073 from C. elegans as similar to
phosphatidyl synthase, is a mistake as this gene does
not contain the C-terminal portion). The physical
connection of the phosphatidyl synthase and the
HAD-superfamily hydrolase domain in S. pombe may,
however, be an important clue to the substrate for the
hydrolases in this equivalog.
Length = 321
Score = 30.6 bits (69), Expect = 0.78
Identities = 19/89 (21%), Positives = 29/89 (32%), Gaps = 17/89 (19%)
Query: 1 MPIFGTKTVITPLNTLILNLTEPQ-----YGKPCLLTFKQVENLFFHFGSLLQRSLTATH 55
+ FG L + L L GKP LT+ E++ + L + +T
Sbjct: 202 LNRFGQGAFRLLLERIYLELNGKPLQYYTLGKPTKLTYDFAEDVLIDWEKRLSGTKPSTS 261
Query: 56 Y------------SDVSGVNNVEWDSVYI 72
SD+ G N W S +
Sbjct: 262 PFHALYMVGDNPASDIIGAQNYGWFSCLV 290
>gnl|CDD|212824 cd11891, MIAL, Melanoma Inhibitory Activity-Like protein. MIAL is
specifically expressed in the cochlea and the vestibule
of the inner ear and may contribute to inner ear
dysfunction in humans. MIAL is a member of the recently
identified family that also includes MIA, MIA2, and MIA3
(also called TANGO); MIA is the most studied member of
the family. MIA is a single domain protein that adopts a
Src Homology 3 (SH3) domain-like fold; it contains an
additional antiparallel beta sheet and two disulfide
bonds compared to classical SH3 domains. MIA is secreted
from malignant melanoma cells and it plays an important
role in melanoma development and invasion. MIA is
expressed by chondrocytes in normal tissues and may be
important in the cartilage cell phenotype. Unlike
classical SH3 domains, MIA does not bind proline-rich
ligands.
Length = 83
Score = 27.1 bits (60), Expect = 3.1
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 9/65 (13%)
Query: 147 LYPLHFGFPIDKYSNLPCRFVEVGSGDLAAGYYSFLWSKLVS---ADIFYAFKEDGEGRL 203
+Y + D Y+ CRF+ + G L +++SKLV A F++ E R
Sbjct: 8 VYAISLARAEDDYNAPDCRFINIKKGQLI-----YVYSKLVKENGAGEFWSGSVYSE-RY 61
Query: 204 EDESG 208
D+ G
Sbjct: 62 VDQMG 66
>gnl|CDD|179622 PRK03646, dadX, alanine racemase; Reviewed.
Length = 355
Score = 27.8 bits (62), Expect = 7.2
Identities = 7/29 (24%), Positives = 12/29 (41%)
Query: 90 LNSHFATGEKLKMTDEQLKALRAHNAGID 118
L SHFA + E + + G++
Sbjct: 155 LMSHFARADHPDGISEAMARIEQAAEGLE 183
>gnl|CDD|222214 pfam13547, GTA_TIM, GTA TIM-barrel-like domain. This domain is
found in the gene transfer agent protein. An unusual
system of genetic exchange exists in the purple
nonsulfur bacterium Rhodobacter capsulatus. DNA
transmission is mediated by a small bacteriophage-like
particle called the gene transfer agent (GTA) that
transfers random 4.5-kb segments of the producing cell's
genome to recipient cells, where allelic replacement
occurs. The genes involved in this process appear to be
found widely in bacteria. According to the SUPERFAMILY
database this domain has a TIM barrel fold.
Length = 296
Score = 27.2 bits (61), Expect = 9.7
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 152 FGFP-IDKYSNLPCRFVEVGSGDLAAGYYS 180
+G P +DK +N P F++ S + A Y+S
Sbjct: 211 YGCPAVDKGTNQPNVFLDPKSSESALPYFS 240
>gnl|CDD|233886 TIGR02481, hemeryth_dom, hemerythrin-like metal-binding domain.
This model describes both members of the hemerythrin
(TIGR00058) family of marine invertebrates and a broader
collection of bacterial and archaeal homologs. Many of
the latter group are multidomain proteins with
signal-transducing domains such as the GGDEF diguanylate
cyclase domain (TIGR00254, pfam00990) and
methyl-accepting chemotaxis protein signaling domain
(pfam00015). Most hemerythrins are oxygen-carriers with
a bound non-heme iron, but at least one example is a
cadmium-binding protein, apparently with a role in
sequestering toxic metals rather than in binding oxygen.
Patterns of conserved residues suggest that all
prokaryotic instances of this domain bind iron or
another heavy metal, but the exact function is unknown.
Not surprisingly, the prokaryote with the most instances
of this domain is Magnetococcus sp. MC-1, a
magnetotactic bacterium.
Length = 126
Score = 26.1 bits (58), Expect = 9.8
Identities = 17/59 (28%), Positives = 23/59 (38%), Gaps = 5/59 (8%)
Query: 72 IINYFLTHFLYEERVFAE-----LNSHFATGEKLKMTDEQLKALRAHNAGIDVCSELFK 125
+I+Y HF EE + E L H EK E+L+ A A + EL
Sbjct: 47 LIDYTENHFADEEELMEEYGYPDLEEHKKEHEKFVKKIEELQEAVAEGADESLAEELLD 105
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 0.140 0.433
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,757,470
Number of extensions: 1303435
Number of successful extensions: 1011
Number of sequences better than 10.0: 1
Number of HSP's gapped: 984
Number of HSP's successfully gapped: 16
Length of query: 265
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 170
Effective length of database: 6,723,972
Effective search space: 1143075240
Effective search space used: 1143075240
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: 58 (26.0 bits)