RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14322
(97 letters)
>gnl|CDD|176471 cd03302, Adenylsuccinate_lyase_2, Adenylsuccinate lyase
(ASL)_subgroup 2. This subgroup contains mainly
eukaryotic proteins similar to ASL, a member of the
Lyase class I family. Members of this family for the
most part catalyze similar beta-elimination reactions in
which a C-N or C-O bond is cleaved with the release of
fumarate as one of the products. These proteins are
active as tetramers. The four active sites of the
homotetrameric enzyme are each formed by residues from
three different subunits. ASL catalyzes two steps in the
de novo purine biosynthesis: the conversion of
5-aminoimidazole-(N-succinylocarboxamide) ribotide
(SAICAR) into 5-aminoimidazole-4-carboxamide ribotide
(AICAR) and, the conversion of adenylsuccinate (SAMP)
into adenosine monophosphate (AMP). ASL deficiency has
been linked to several pathologies including psychomotor
retardation with autistic features, epilepsy and muscle
wasting.
Length = 436
Score = 65.8 bits (161), Expect = 3e-14
Identities = 24/33 (72%), Positives = 28/33 (84%)
Query: 1 MDEQAISRARDELRFRGVKGTTGTQASFLELFN 33
MD + + R RD+LRFRGVKGTTGTQASFL+LF
Sbjct: 165 MDLRNLERLRDDLRFRGVKGTTGTQASFLDLFE 197
Score = 65.0 bits (159), Expect = 7e-14
Identities = 22/42 (52%), Positives = 31/42 (73%)
Query: 47 RSRVKQHGKENDLVDRIRADPYFAPILNQMPTLLDPKSFYGR 88
+ VKQ G +NDL++RI+ D YF PI +++ LLDPK+F GR
Sbjct: 395 AAVVKQEGGDNDLIERIKNDAYFKPIWDELDALLDPKTFIGR 436
>gnl|CDD|198066 smart00998, ADSL_C, Adenylosuccinate lyase C-terminus.
Adenylosuccinate lyase catalyses two steps in the
synthesis of purine nucleotides: the conversion of
succinylaminoimidazole-carboxamide ribotide into
aminoimidazole-carboxamide ribotide (the fifth step of
de novo IMP biosynthesis); the formation of adenosine
monophosphate (AMP) from adenylosuccinate (the final
step in the synthesis of AMP from IMP). This entry
represents the C-terminal, seven alpha-helical, domain
of adenylosuccinate lyase.
Length = 81
Score = 35.9 bits (84), Expect = 3e-04
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 58 DLVDRIRADPYFAPILN--QMPTLLDPKSFYGRAPEQV 93
DL + + ADP L+ ++ L DP+ + G A V
Sbjct: 40 DLRELLLADPEVTAYLSEEELEELFDPEYYLGHADAIV 77
>gnl|CDD|176467 cd01595, Adenylsuccinate_lyase_like, Adenylsuccinate lyase
(ASL)_like. This group contains ASL, prokaryotic-type
3-carboxy-cis,cis-muconate cycloisomerase (pCMLE), and
related proteins. These proteins are members of the
Lyase class I family. Members of this family for the
most part catalyze similar beta-elimination reactions in
which a C-N or C-O bond is cleaved with the release of
fumarate as one of the products. These proteins are
active as tetramers. The four active sites of the
homotetrameric enzyme are each formed by residues from
three different subunits. ASL catalyzes two steps in the
de novo purine biosynthesis: the conversion of
5-aminoimidazole-(N-succinylocarboxamide) ribotide
(SAICAR) into 5-aminoimidazole-4-carboxamide ribotide
(AICAR) and; the conversion of adenylsuccinate (SAMP)
into adenosine monophosphate (AMP). pCMLE catalyzes the
cyclization of 3-carboxy-cis,cis-muconate (3CM) to
4-carboxy-muconolactone, in the beta-ketoadipate
pathway. ASL deficiency has been linked to several
pathologies including psychomotor retardation with
autistic features, epilepsy and muscle wasting.
Length = 381
Score = 37.1 bits (87), Expect = 4e-04
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 1 MDEQAISRARDELRFRGVKGTTGTQASFLE 30
+ + AR+ + G+ G GT AS
Sbjct: 158 RHLERLEEARERVLVGGISGAVGTHASLGP 187
>gnl|CDD|220731 pfam10397, ADSL_C, Adenylosuccinate lyase C-terminus. This is
the C-terminal seven alpha helices of the structure
whose full length represents the enzyme
adenylosuccinate lyase. This sequence lies C-terminal
to the conserved motif necessary for beta-elimination
reactions, Adenylosuccinate lyase catalyzes two steps
in the synthesis of purine nucleotides: the conversion
of succinylaminoimidazole-carboxamide ribotide into
aminoimidazole-carboxamide ribotide, the eighth step of
the de novo pathway, and the formation of adenosine
monophosphate (AMP) from adenylosuccinate, the second
step in the conversion of inosine monophosphate into
AMP.
Length = 80
Score = 34.7 bits (81), Expect = 7e-04
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 56 ENDLVDRIRADPYFAPILN--QMPTLLDPKSFYGRAPEQV 93
DL + + ADP A L+ ++ L DP + G A V
Sbjct: 37 GRDLREVLLADPEVAAYLSEEELDALFDPAYYLGHADAIV 76
>gnl|CDD|233192 TIGR00928, purB, adenylosuccinate lyase. This family consists of
adenylosuccinate lyase, the enzyme that catalyzes step 8
in the purine biosynthesis pathway for de novo synthesis
of IMP and also the final reaction in the two-step
sequence from IMP to AMP [Purines, pyrimidines,
nucleosides, and nucleotides, Purine ribonucleotide
biosynthesis].
Length = 435
Score = 35.4 bits (82), Expect = 0.002
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 8/60 (13%)
Query: 45 SPRSRVKQHGK------ENDLVDRIRADPYFAPILNQ--MPTLLDPKSFYGRAPEQVVDV 96
V++ E DL++ + AD L + + LLDP+++ G A E V V
Sbjct: 376 EAYEIVRELAMGAAEVDEPDLLEFLLADERITKYLKEEELAELLDPETYIGNAREIVERV 435
Score = 31.6 bits (72), Expect = 0.039
Identities = 12/60 (20%), Positives = 28/60 (46%), Gaps = 8/60 (13%)
Query: 8 RARDELRFRGVKGTTGTQASFLELFNDI------TLQFATSPFSPRSRVKQHGKENDLVD 61
+A++ ++ G+ G GT A+ L ++ L P S ++++ + +L+D
Sbjct: 173 QAKERIKVGGISGAVGTHAAAYPLVEEVEERVTEFLGLKPVPIS--TQIEPRDRHAELLD 230
>gnl|CDD|223094 COG0015, PurB, Adenylosuccinate lyase [Nucleotide transport and
metabolism].
Length = 438
Score = 33.4 bits (77), Expect = 0.011
Identities = 6/32 (18%), Positives = 15/32 (46%)
Query: 4 QAISRARDELRFRGVKGTTGTQASFLELFNDI 35
+ + A + + + G GT A+ +L ++
Sbjct: 170 ERLEEAEERIIVGKIGGAVGTLAALGDLGAEV 201
>gnl|CDD|180802 PRK07035, PRK07035, short chain dehydrogenase; Provisional.
Length = 252
Score = 29.2 bits (66), Expect = 0.27
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 51 KQHGKENDLVDRIRADPYFAPILN 74
++HG+ + LV+ A+PYF IL+
Sbjct: 81 ERHGRLDILVNNAAANPYFGHILD 104
>gnl|CDD|237263 PRK12999, PRK12999, pyruvate carboxylase; Reviewed.
Length = 1146
Score = 26.3 bits (59), Expect = 2.7
Identities = 15/31 (48%), Positives = 17/31 (54%), Gaps = 7/31 (22%)
Query: 3 EQAISRAR---DELRFRGVKGTTGTQASFLE 30
EQA++R R E R RGVK T FLE
Sbjct: 408 EQAVARMRRALREFRIRGVK----TNIPFLE 434
>gnl|CDD|236352 PRK08937, PRK08937, adenylosuccinate lyase; Provisional.
Length = 216
Score = 25.8 bits (57), Expect = 3.4
Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 7/46 (15%)
Query: 49 RVKQH-----GKENDLVDRIRADPYFAPILNQ--MPTLLDPKSFYG 87
+++ + DL + + AD F L + + L DP++F G
Sbjct: 171 LIREKAMEAWKNQKDLRELLEADERFTKQLTKEELDELFDPEAFVG 216
>gnl|CDD|226742 COG4292, COG4292, Predicted membrane protein [Function unknown].
Length = 387
Score = 25.9 bits (57), Expect = 3.8
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 19 KGTTGTQASFLELFNDITLQFA 40
+ + SFLELF D+ FA
Sbjct: 13 EALDEKKVSFLELFFDLIFVFA 34
>gnl|CDD|233427 TIGR01472, gmd, GDP-mannose 4,6-dehydratase. Alternate name:
GDP-D-mannose dehydratase. This enzyme converts
GDP-mannose to GDP-4-dehydro-6-deoxy-D-mannose, the
first of three steps for the conversion of GDP-mannose
to GDP-fucose in animals, plants, and bacteria. In
bacteria, GDP-L-fucose acts as a precursor of surface
antigens such as the extracellular polysaccharide
colanic acid of E. coli. Excluded from this model are
members of the clade that score poorly because of highly
dervied (phylogenetically long-branch) sequences, e.g.
Aneurinibacillus thermoaerophilus Gmd, described as a
bifunctional GDP-mannose
4,6-dehydratase/GDP-6-deoxy-D-lyxo-4-hexulose reductase
(PUBMED:11096116) [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 343
Score = 26.0 bits (57), Expect = 4.1
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 25 QASFLELFNDITL--QFATSPFSPRS 48
QAS EL+ + Q T+PF PRS
Sbjct: 129 QASTSELYGKVQEIPQNETTPFYPRS 154
>gnl|CDD|224661 COG1747, COG1747, Uncharacterized N-terminal domain of the
transcription elongation factor GreA [Function unknown].
Length = 711
Score = 25.3 bits (55), Expect = 6.6
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 34 DITLQFATSPFSPRSR-----VKQHGKENDLVDRIRADPYFA 70
DI+ + A S P S+ +K+ G +DL R DP +A
Sbjct: 324 DISFEMAFSALQPLSKEDIFVLKRVGDPDDLAAFARKDPEWA 365
>gnl|CDD|237053 PRK12315, PRK12315, 1-deoxy-D-xylulose-5-phosphate synthase;
Provisional.
Length = 581
Score = 25.0 bits (55), Expect = 8.2
Identities = 11/39 (28%), Positives = 18/39 (46%)
Query: 59 LVDRIRADPYFAPILNQMPTLLDPKSFYGRAPEQVVDVD 97
L+ +I+ I +P + K F + P+Q VDV
Sbjct: 288 LLKKIKEGKPVVAINAAIPGVFGLKEFRKKYPDQYVDVG 326
>gnl|CDD|221503 pfam12275, DUF3616, Protein of unknown function (DUF3616). This
family of proteins is found in bacteria. Proteins in
this family are typically between 335 and 392 amino
acids in length. There is a conserved GLRGPV sequence
motif.
Length = 331
Score = 24.7 bits (54), Expect = 8.7
Identities = 7/26 (26%), Positives = 11/26 (42%)
Query: 49 RVKQHGKENDLVDRIRADPYFAPILN 74
+K + N L + DP+ P L
Sbjct: 137 MLKGDKRGNLLTAALADDPHLGPFLA 162
>gnl|CDD|236283 PRK08540, PRK08540, adenylosuccinate lyase; Reviewed.
Length = 449
Score = 24.9 bits (55), Expect = 9.1
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 79 LLDPKSFYGRAPEQV 93
LLDP+++ G APE V
Sbjct: 423 LLDPETYIGTAPEIV 437
>gnl|CDD|131764 TIGR02717, AcCoA-syn-alpha, acetyl coenzyme A synthetase (ADP
forming), alpha domain. Although technically
reversible, it is believed that this group of
ADP-dependent acetyl-CoA synthetases (ACS) act in the
direction of acetate and ATP production in the organisms
in which it has been characterized. In most species this
protein exists as a fused alpha-beta domain polypeptide.
In Pyrococcus and related species, however the domains
exist as separate polypeptides. This model represents
the alpha (N-terminal) domain. In Pyrococcus and related
species there appears to have been the development of a
paralogous family such that four other proteins are
close relatives. In reference , one of these (along with
its beta-domain partner) was characterized as ACS-II
showing specificity for phenylacetyl-CoA. This model has
been constructed to exclude these non-ACS-I paralogs.
This may result in new, authentic ACS-I sequences
falling below the trusted cutoff.
Length = 447
Score = 25.0 bits (55), Expect = 9.1
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 55 KENDLVDRIRADPYFAPILNQMPTLLDPKSFYGRAPE 91
E+DL++ + DP IL + + D + F A E
Sbjct: 190 DESDLLEYLADDPDTKVILLYLEGIKDGRKFLKTARE 226
>gnl|CDD|184560 PRK14190, PRK14190, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 284
Score = 24.6 bits (54), Expect = 9.1
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 3/41 (7%)
Query: 58 DLVDRIRADPYFAPILNQM--PTLLDPKSFYGR-APEQVVD 95
L+DR+ ADP IL Q+ P +D K+ R +PE+ VD
Sbjct: 80 ALIDRLNADPRINGILVQLPLPKHIDEKAVIERISPEKDVD 120
>gnl|CDD|176469 cd01597, pCLME, prokaryotic 3-carboxy-cis,cis-muconate
cycloisomerase (CMLE)_like. This subgroup contains
pCLME and related proteins, and belongs to the Lyase
class I family. Members of this family for the most part
catalyze similar beta-elimination reactions in which a
C-N or C-O bond is cleaved with the release of fumarate
as one of the products. These proteins are active as
tetramers. The four active sites of the homotetrameric
enzyme are each formed by residues from three different
subunits. CMLE catalyzes the cyclization of
3-carboxy-cis,cis-muconate (3CM) to
4-carboxy-muconolactone in the beta-ketoadipate pathway.
This pathway is responsible for the catabolism of a
variety of aromatic compounds into intermediates of the
citric cycle in prokaryotic and eukaryotic
micro-organisms.
Length = 437
Score = 24.9 bits (55), Expect = 9.4
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 58 DLVDRIRADPYFAPILN--QMPTLLDPKSFYGRAPEQVVDV 96
L + + DP A L+ ++ LLDP ++ G AP V V
Sbjct: 394 PLREVLLEDPEVAAYLSDEELDALLDPANYLGSAPALVDRV 434
>gnl|CDD|132123 TIGR03079, CH4_NH3mon_ox_B, methane monooxygenase/ammonia
monooxygenase, subunit B. Both ammonia oxidizers such
as Nitrosomonas europaea and methanotrophs (obligate
methane oxidizers) such as Methylococcus capsulatus each
can grow only on their own characteristic substrate.
However, both groups have the ability to oxidize both
substrates, and so the relevant enzymes must be named
here according to their ability to oxidze both. The
protein family represented here reflects subunit B of
both the particulate methane monooxygenase of
methylotrophs and the ammonia monooxygenase of
nitrifying bacteria.
Length = 399
Score = 24.9 bits (54), Expect = 9.7
Identities = 12/24 (50%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 39 FATSP-FSPRSRVKQHGKENDLVD 61
FA P F PRSRV +N L+D
Sbjct: 193 FAARPMFLPRSRVLLAYGDNLLLD 216
>gnl|CDD|132268 TIGR03224, benzo_boxA, benzoyl-CoA oxygenase/reductase, BoxA
protein. Members of this protein family are BoxA, the A
component of the BoxAB benzoyl-CoA oxygenase/reductase.
This oxygen-requiring enzyme acts in an aerobic pathway
of benzoate catabolism via coenzyme A ligation. BoxA is
a homodimeric iron-sulphur-flavoprotein and acts as an
NADPH-dependent reductase for BoxB [Energy metabolism,
Other].
Length = 411
Score = 24.8 bits (54), Expect = 10.0
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 5/51 (9%)
Query: 47 RSRVKQHGKENDLV----DRIRAD-PYFAPILNQMPTLLDPKSFYGRAPEQ 92
R R + HG+ L+ R + + PYF P+ +D + R PEQ
Sbjct: 289 RRRRRDHGEGGKLMLFFGARTKEELPYFGPLQKLPKDFIDINFAFSRTPEQ 339
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
0.320 0.137 0.393
Gapped
Lambda K H
0.267 0.0865 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,099,518
Number of extensions: 417302
Number of successful extensions: 366
Number of sequences better than 10.0: 1
Number of HSP's gapped: 363
Number of HSP's successfully gapped: 25
Length of query: 97
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 33
Effective length of database: 8,098,946
Effective search space: 267265218
Effective search space used: 267265218
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 (21.8 bits)
S2: 53 (23.9 bits)