RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3940
(83 letters)
>gnl|CDD|216084 pfam00725, 3HCDH, 3-hydroxyacyl-CoA dehydrogenase, C-terminal
domain. This family also includes lambda crystallin.
Some proteins include two copies of this domain.
Length = 97
Score = 107 bits (269), Expect = 2e-32
Identities = 39/81 (48%), Positives = 54/81 (66%), Gaps = 1/81 (1%)
Query: 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDA 60
+ E G A+P DID AM+LG G PMGPFEL+D VG D I++ ++F + ++P
Sbjct: 18 LVEEGVATPEDIDAAMRLGLGLPMGPFELSDLVGLDVGYHILEVLAEEFGD-RAYRPSPL 76
Query: 61 LNKLVDEGKLGVKSGEGFYNY 81
L KLV+ G+LG K+G+GFY Y
Sbjct: 77 LEKLVEAGRLGRKTGKGFYKY 97
>gnl|CDD|224170 COG1250, FadB, 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism].
Length = 307
Score = 108 bits (273), Expect = 1e-30
Identities = 38/83 (45%), Positives = 55/83 (66%)
Query: 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDA 60
+ E G A+P +ID AM+ G G PMGPFELAD +G D I+ ++ ++P ++P
Sbjct: 203 LLEEGVATPEEIDAAMRQGLGLPMGPFELADLIGLDVMLHIMKVLNETLGDDPYYRPPPL 262
Query: 61 LNKLVDEGKLGVKSGEGFYNYKK 83
L KLV+ G+LG KSG+GFY+Y+
Sbjct: 263 LRKLVEAGRLGRKSGKGFYDYRG 285
>gnl|CDD|215300 PLN02545, PLN02545, 3-hydroxybutyryl-CoA dehydrogenase.
Length = 295
Score = 103 bits (258), Expect = 1e-28
Identities = 36/83 (43%), Positives = 48/83 (57%), Gaps = 1/83 (1%)
Query: 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDA 60
G AS DIDT MKLG +PMGP LAD++G DT I+ H+ ++ ++P
Sbjct: 204 ALYTGVASKEDIDTGMKLGTNHPMGPLHLADFIGLDTCLSIMKVLHEGLGDSK-YRPCPL 262
Query: 61 LNKLVDEGKLGVKSGEGFYNYKK 83
L + VD G+LG KSG G Y+Y
Sbjct: 263 LVQYVDAGRLGRKSGRGVYHYDG 285
>gnl|CDD|181133 PRK07819, PRK07819, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 286
Score = 98.5 bits (246), Expect = 7e-27
Identities = 41/81 (50%), Positives = 51/81 (62%), Gaps = 1/81 (1%)
Query: 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDA 60
M E G A+ DID AM LG +PMGP L+D VG DT K I D +++F E PL+ P
Sbjct: 207 MVESGFATAEDIDKAMVLGCAHPMGPLRLSDLVGLDTVKAIADSMYEEFKE-PLYAPPPL 265
Query: 61 LNKLVDEGKLGVKSGEGFYNY 81
L ++V+ G LG KSG GFY Y
Sbjct: 266 LLRMVEAGLLGKKSGRGFYTY 286
>gnl|CDD|180269 PRK05808, PRK05808, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 282
Score = 83.5 bits (207), Expect = 3e-21
Identities = 33/80 (41%), Positives = 47/80 (58%), Gaps = 1/80 (1%)
Query: 2 YERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDAL 61
G A+ DID MKLG +P+GP LAD +G DT I++ ++ F + ++P L
Sbjct: 204 LAEGVATAEDIDEGMKLGCNHPIGPLALADLIGLDTCLAIMEVLYEGF-GDSKYRPCPLL 262
Query: 62 NKLVDEGKLGVKSGEGFYNY 81
K+V G LG K+G GFY+Y
Sbjct: 263 RKMVAAGWLGRKTGRGFYDY 282
>gnl|CDD|236434 PRK09260, PRK09260, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 288
Score = 79.4 bits (196), Expect = 1e-19
Identities = 34/81 (41%), Positives = 46/81 (56%), Gaps = 2/81 (2%)
Query: 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDA 60
M + G A+ DID A++LG +PMGP EL D VG DT + H+ E ++P
Sbjct: 202 MLQEGVATAEDIDKAIRLGLNFPMGPLELGDLVGLDTRLNNLKYLHETLGEK--YRPAPL 259
Query: 61 LNKLVDEGKLGVKSGEGFYNY 81
L K V G+LG K+G G Y+Y
Sbjct: 260 LEKYVKAGRLGRKTGRGVYDY 280
>gnl|CDD|181359 PRK08293, PRK08293, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 287
Score = 79.2 bits (196), Expect = 1e-19
Identities = 33/79 (41%), Positives = 42/79 (53%)
Query: 4 RGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNK 63
+G A P ID + G PMGPF + D VG DT I W + + K L +
Sbjct: 209 KGVADPETIDKTWMIATGAPMGPFGILDIVGLDTAYNITSNWAEATDDENAKKAAALLKE 268
Query: 64 LVDEGKLGVKSGEGFYNYK 82
+D+GKLGV +GEGFYNY
Sbjct: 269 YIDKGKLGVATGEGFYNYP 287
>gnl|CDD|181018 PRK07530, PRK07530, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 292
Score = 76.6 bits (189), Expect = 1e-18
Identities = 39/82 (47%), Positives = 52/82 (63%), Gaps = 2/82 (2%)
Query: 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDA 60
+YE G S IDTAMKLGA +PMGP ELAD++G DT I+ H ++ ++P
Sbjct: 205 LYE-GVGSVEAIDTAMKLGANHPMGPLELADFIGLDTCLSIMQVLHDGLADSK-YRPCPL 262
Query: 61 LNKLVDEGKLGVKSGEGFYNYK 82
L K V+ G LG K+G GFY+Y+
Sbjct: 263 LVKYVEAGWLGRKTGRGFYDYR 284
>gnl|CDD|236211 PRK08268, PRK08268, 3-hydroxy-acyl-CoA dehydrogenase; Validated.
Length = 507
Score = 76.0 bits (188), Expect = 5e-18
Identities = 33/85 (38%), Positives = 47/85 (55%), Gaps = 8/85 (9%)
Query: 1 MYERGDASPRDIDTAMKLGAGYPMGPFELADYVGHD----TTKFIIDGWHKKFPENPLFK 56
+ E G A P ID ++ AG+ MGPFEL D +G D + + + +F + P F+
Sbjct: 207 VLEEGVADPATIDAILREAAGFRMGPFELMDLIGLDVNHAVMESV---YR-QFYQEPRFR 262
Query: 57 PVDALNKLVDEGKLGVKSGEGFYNY 81
P +LV G+LG KSG+GFY Y
Sbjct: 263 PSLIQQELVAAGRLGRKSGQGFYRY 287
Score = 56.0 bits (136), Expect = 7e-11
Identities = 17/30 (56%), Positives = 20/30 (66%)
Query: 5 GDASPRDIDTAMKLGAGYPMGPFELADYVG 34
G ASP DID AM+LG YP+GP D +G
Sbjct: 437 GIASPADIDLAMRLGLNYPLGPLAWGDRLG 466
>gnl|CDD|188207 TIGR02279, PaaC-3OHAcCoADH, 3-hydroxyacyl-CoA dehydrogenase PaaC.
This 3-hydroxyacyl-CoA dehydrogenase is involved in the
degradation of phenylacetic acid, presumably in steps
following the opening of the phenyl ring. The sequences
included in this model are all found in aparrent operons
with other related genes such as paaA, paaB, paaD, paaE,
paaF and paaN. Some genomes contain these other genes
without an apparent paaC in the same operon - possibly
in these cases a different dehydrogenase involved in
fatty acid degradation may fill in the needed activity.
This enzyme has domains which are members of the
pfam02737 and pfam00725 families.
Length = 503
Score = 72.7 bits (178), Expect = 8e-17
Identities = 33/84 (39%), Positives = 47/84 (55%), Gaps = 8/84 (9%)
Query: 3 ERGDASPRDIDTAMKLGAGYPMGPFELADYVGHD----TTKFIIDGWHKKFPENPLFKPV 58
E A+P +D A++ GAG+PMGPFEL D +GHD T + + + + F P
Sbjct: 207 EEQVAAPAVLDAALRDGAGFPMGPFELTDLIGHDVNFAVTCSVFNAFWQDRR----FLPS 262
Query: 59 DALNKLVDEGKLGVKSGEGFYNYK 82
+LV G+LG KSG G Y+Y+
Sbjct: 263 LVQQELVIAGRLGRKSGLGVYDYR 286
Score = 43.0 bits (101), Expect = 2e-06
Identities = 17/31 (54%), Positives = 21/31 (67%)
Query: 4 RGDASPRDIDTAMKLGAGYPMGPFELADYVG 34
+G AS +DIDTAM+LG YP GP A +G
Sbjct: 435 QGVASAQDIDTAMRLGVNYPYGPLAWAAQLG 465
>gnl|CDD|180361 PRK06035, PRK06035, 3-hydroxyacyl-CoA dehydrogenase; Validated.
Length = 291
Score = 56.0 bits (135), Expect = 5e-11
Identities = 33/85 (38%), Positives = 51/85 (60%), Gaps = 6/85 (7%)
Query: 2 YERGDASPRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDAL 61
+E G A+ +DID KL G+PMGPFEL D +G DT I + +++ + P F P ++L
Sbjct: 207 FEIGIATIKDIDEMCKLAFGFPMGPFELMDIIGIDTVYHIAEYLYEETGD-PQFIPPNSL 265
Query: 62 NKLVDEGKLG---VKSGE--GFYNY 81
++V G +G VK G G+++Y
Sbjct: 266 KQMVLNGYVGDKKVKYGSKGGWFDY 290
>gnl|CDD|235707 PRK06130, PRK06130, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 311
Score = 54.4 bits (131), Expect = 2e-10
Identities = 29/82 (35%), Positives = 40/82 (48%), Gaps = 5/82 (6%)
Query: 3 ERGDASPRDIDTAMKLGAGYPM---GPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVD 59
E+G AS DID +K G + GP E D G D + ++ EN P
Sbjct: 203 EKGVASAEDIDEVVKWSLGIRLALTGPLEQRDMNGLDVHLAVASYLYQDL-ENRT-TPSP 260
Query: 60 ALNKLVDEGKLGVKSGEGFYNY 81
L + V+ G+LG KSG+GFY +
Sbjct: 261 LLEEKVEAGELGAKSGQGFYAW 282
>gnl|CDD|236864 PRK11154, fadJ, multifunctional fatty acid oxidation complex
subunit alpha; Reviewed.
Length = 708
Score = 54.5 bits (132), Expect = 2e-10
Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 11 DIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKL 70
ID A+ + G+P+GP L D VG D II E F A +KL+++ +
Sbjct: 519 HIDAAL-VKFGFPVGPITLLDEVGIDVGTKIIPILEAALGER--FSAPAAFDKLLNDDRK 575
Query: 71 GVKSGEGFYNYKK 83
G K+G GFY Y +
Sbjct: 576 GRKNGRGFYLYGQ 588
>gnl|CDD|183293 PRK11730, fadB, multifunctional fatty acid oxidation complex
subunit alpha; Reviewed.
Length = 715
Score = 53.7 bits (130), Expect = 4e-10
Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 4/76 (5%)
Query: 10 RDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPE--NPLFKPVDALNKLVDE 67
R ID M+ G+PMGP L D VG DT + FP+ ++ DA++ L +
Sbjct: 521 RQIDKVMEKQFGWPMGPAYLLDVVGIDTAHHAQAVMAEGFPDRMKKDYR--DAIDVLFEA 578
Query: 68 GKLGVKSGEGFYNYKK 83
+ G K+G+GFY Y++
Sbjct: 579 KRFGQKNGKGFYRYEE 594
Score = 24.8 bits (55), Expect = 6.3
Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 15/78 (19%)
Query: 7 ASPRDIDTAMKLGAGYPM---GPFELADYVGHDTTKFIIDGWHKKFPE-NPLFKPVDALN 62
ASP + D A+ G G+P G F D +G ++ K+ PL++ + L
Sbjct: 649 ASPAEADMALVYGLGFPPFRGGAFRYLDTLG--VANYV--ALADKYAHLGPLYQVPEGLR 704
Query: 63 KLVDEGKLGVKSGEGFYN 80
++ +GE +Y
Sbjct: 705 EM-------AANGESYYP 715
>gnl|CDD|131490 TIGR02437, FadB, fatty oxidation complex, alpha subunit FadB.
Members represent alpha subunit of multifunctional
enzyme complex of the fatty acid degradation cycle.
Activities include: enoyl-CoA hydratase (EC 4.2.1.17),
dodecenoyl-CoA delta-isomerase activity (EC 5.3.3.8),
3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35),
3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A
representative is E. coli FadB. This model excludes the
FadJ family represented by SP:P77399 [Fatty acid and
phospholipid metabolism, Degradation].
Length = 714
Score = 50.6 bits (121), Expect = 5e-09
Identities = 27/73 (36%), Positives = 38/73 (52%)
Query: 10 RDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGK 69
ID M+ G+PMGP L D VG DT + FP+ DA++ L + +
Sbjct: 521 VRIDKVMEKQFGWPMGPAYLLDVVGIDTGHHAQAVMAEGFPDRMGKDGRDAIDALFEAKR 580
Query: 70 LGVKSGEGFYNYK 82
LG K+G+GFY Y+
Sbjct: 581 LGQKNGKGFYAYE 593
>gnl|CDD|181340 PRK08269, PRK08269, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 314
Score = 47.7 bits (114), Expect = 4e-08
Identities = 26/88 (29%), Positives = 43/88 (48%), Gaps = 12/88 (13%)
Query: 1 MYERGDASPRDIDTAMKLGAGYP---MGPFELADYVGHDT----TKFIIDGWHKKFPENP 53
M E G AS DID A++ G G +G E D+ G D ++++
Sbjct: 200 MVEEGVASAEDIDKAIRTGFGLRFAVLGLLEFIDWGGCDILYYASRYLAGEIGPD----- 254
Query: 54 LFKPVDALNKLVDEGKLGVKSGEGFYNY 81
F P + + ++EG+ G+++G GFY+Y
Sbjct: 255 RFAPPAIVVRNMEEGRDGLRTGAGFYDY 282
>gnl|CDD|131493 TIGR02440, FadJ, fatty oxidation complex, alpha subunit FadJ.
Members represent alpha subunit of multifunctional
enzyme complex of the fatty acid degradation cycle.
Plays a minor role in aerobic beta-oxidation of fatty
acids. FadJI complex is necessary for anaerobic growth
on short-chain acids with nitrate as an electron
acceptor. Activities include: enoyl-CoA hydratase (EC
4.2.1.17),3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35),
3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A
representative is E. coli FadJ (aka YfcX). This model
excludes the FadB of TIGR02437 equivalog model [Fatty
acid and phospholipid metabolism, Degradation].
Length = 699
Score = 44.0 bits (104), Expect = 1e-06
Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 12 IDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLG 71
ID A+ + G+P+GP L D VG D I + E FK +KL+ + + G
Sbjct: 515 IDKAL-VKFGFPVGPITLLDEVGIDVGAKISPILEAELGER--FKAPAVFDKLLSDDRKG 571
Query: 72 VKSGEGFYNY 81
K+G+GFY Y
Sbjct: 572 RKNGKGFYLY 581
Score = 28.2 bits (63), Expect = 0.39
Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 7 ASPRDIDTAMKLGAGYPM---GPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNK 63
SPRD D G G+P GPF D +G D I++ ++ + F P L
Sbjct: 633 RSPRDGDIGAIFGIGFPPFLGGPFRYIDTLGADNVVKILERLQTQYGDR--FTPCQRLVA 690
Query: 64 LVDEGK 69
+ E +
Sbjct: 691 MAAEKQ 696
>gnl|CDD|131494 TIGR02441, fa_ox_alpha_mit, fatty acid oxidation complex, alpha
subunit, mitochondrial. Members represent alpha subunit
of mitochondrial multifunctional fatty acid degradation
enzyme complex. Subunit activities include: enoyl-CoA
hydratase (EC 4.2.1.17) & 3-hydroxyacyl-CoA
dehydrogenase (EC 1.1.1.35). Some characterization in
human , pig , and rat. The beta subunit has activity:
acetyl-CoA C-acyltransferase (EC 2.3.1.16).
Length = 737
Score = 42.9 bits (101), Expect = 3e-06
Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 9 PRDIDTAMKLGAGYPMGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEG 68
P+ +D + G+P+G LAD VG D + + + K F E + L++LV G
Sbjct: 542 PKKLD-KLTTKFGFPVGAATLADEVGVDVAEHVAEDLGKAFGERFGGGSAELLSELVKAG 600
Query: 69 KLGVKSGEGFYNY 81
LG KSG+G + Y
Sbjct: 601 FLGRKSGKGIFIY 613
>gnl|CDD|235706 PRK06129, PRK06129, 3-hydroxyacyl-CoA dehydrogenase; Validated.
Length = 308
Score = 31.9 bits (73), Expect = 0.018
Identities = 16/45 (35%), Positives = 20/45 (44%), Gaps = 12/45 (26%)
Query: 1 MYERGDASPRDIDTAMKLGAGYP---MGPFE---------LADYV 33
+ G AS DID ++ G G MGPFE +ADY
Sbjct: 204 LVADGVASVDDIDAVIRDGLGLRWSFMGPFETIDLNAPGGVADYA 248
>gnl|CDD|184886 PRK14892, PRK14892, putative transcription elongation factor
Elf1; Provisional.
Length = 99
Score = 30.4 bits (69), Expect = 0.032
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 44 GWHKKFPENPLFKPVDALNKLVD---EGKLGVK 73
G + +F ++ VD NK +D EGK+ +K
Sbjct: 49 GLYTEFEVPSVYDEVDVYNKFIDLYLEGKIEIK 81
>gnl|CDD|201202 pfam00392, GntR, Bacterial regulatory proteins, gntR family.
This family of regulatory proteins consists of the
N-terminal HTH region of GntR-like bacterial
transcription factors. At the C-terminus there is
usually an effector-binding/oligomerisation domain. The
GntR-like proteins include the following sub-families:
MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many
of these proteins have been shown experimentally to be
autoregulatory, enabling the prediction of operator
sites and the discovery of cis/trans relationships. The
DasR regulator has been shown to be a global regulator
of primary metabolism and development in Streptomyces
coelicolor.
Length = 64
Score = 28.7 bits (65), Expect = 0.093
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 59 DALNKLVDEGKLGVKSGEGFY 79
+AL +L EG + + G G +
Sbjct: 43 EALRRLEAEGLVERRQGRGTF 63
>gnl|CDD|202361 pfam02728, Cu_amine_oxidN3, Copper amine oxidase, N3 domain.
This domain is the second or third structural domain in
copper amine oxidases, it is known as the N3 domain.
Its function is uncertain. The catalytic domain can be
found in pfam01179. Copper amine oxidases are a
ubiquitous and novel group of quinoenzymes that
catalyze the oxidative deamination of primary amines to
the corresponding aldehydes, with concomitant reduction
of molecular oxygen to hydrogen peroxide. The enzymes
are dimers of identical 70-90 kDa subunits, each of
which contains a single copper ion and a covalently
bound cofactor formed by the post-translational
modification of a tyrosine side chain to
2,4,5-trihydroxyphenylalanine quinone (TPQ).
Length = 101
Score = 26.9 bits (60), Expect = 0.63
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 24 MGPFELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVD 66
+G F A G K + +++ N P++ L LVD
Sbjct: 43 VGWFGEASE-GRRLLKALC--YYRDGTVNFYAHPIEGLEILVD 82
>gnl|CDD|236159 PRK08134, PRK08134, O-acetylhomoserine
aminocarboxypropyltransferase; Validated.
Length = 433
Score = 27.0 bits (60), Expect = 0.92
Identities = 21/62 (33%), Positives = 27/62 (43%), Gaps = 20/62 (32%)
Query: 22 YPMGPFEL-ADYVGHDTTKF-----------IIDG----WHK--KFPENPLFKPVDALNK 63
Y + PFE AD V H TKF ++DG W KFPE L +P +
Sbjct: 192 YLLRPFEHGADLVYHSATKFLGGHGTAIGGVLVDGGRFDWEASGKFPE--LTEPYAGFHG 249
Query: 64 LV 65
+V
Sbjct: 250 MV 251
>gnl|CDD|215817 pfam00248, Aldo_ket_red, Aldo/keto reductase family. This family
includes a number of K+ ion channel beta chain
regulatory domains - these are reported to have
oxidoreductase activity.
Length = 277
Score = 26.9 bits (60), Expect = 1.0
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 46 HKKFPENPLFKPVDALNKLVDEGKLG 71
H P P+ + ++AL +L EGK+
Sbjct: 105 HWPDPSLPIEETLEALEELKKEGKIR 130
>gnl|CDD|217383 pfam03136, Pup_ligase, Pup-ligase protein. Pupylation is a novel
protein modification system found in some bacteria. This
family of proteins are the enzyme that can conjugate
proteins of the Pup family to lysine residues in target
proteins marking them for degradation. The archetypal
protein in this family is PafA (proteasome accessory
factor) from Mycobacterium tuberculosis. It has been
suggested that these proteins are related to
gamma-glutamyl-cysteine synthetases.
Length = 445
Score = 26.9 bits (60), Expect = 1.1
Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 16/50 (32%)
Query: 5 GDASPRDIDTAMKLG----------AGYPMGPFELADYVG------HDTT 38
GD++ + T +K+G AG + LAD V HD T
Sbjct: 233 GDSNMSETSTYLKVGTTSLVLDMIEAGVDLPDLSLADPVRAIRAISHDLT 282
>gnl|CDD|227225 COG4888, COG4888, Uncharacterized Zn ribbon-containing protein
[General function prediction only].
Length = 104
Score = 26.3 bits (58), Expect = 1.2
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 3/30 (10%)
Query: 49 FPENPLFKPVDALNKLVD---EGKLGVKSG 75
L +PVD + VD EG+ +SG
Sbjct: 58 CEVPELSEPVDVYSAWVDAYLEGRGCGESG 87
>gnl|CDD|211388 cd11302, O-FucT-1, GDP-fucose protein O-fucosyltransferase 1. The
protein O-fucosyltransferase 1 (Ofut1 or O-FucT-1) adds
O-fucose to EGF (epidermal growth factor-like) repeats.
The O-fucsosylation of the Notch receptor signaling
protein is dependent on this enzyme, which requires
GDP-fucose as a substrate. O-fucose residues added to
the target of O-FucT-1 may be further elongated by other
glycosyltransferases. On top of O-fucosylation, O-FucT-1
may have other functions such as the regulation of the
Notch receptor exit from the ER. Six highly conserved
cysteines are present in O-FucT-1, which is a soluble ER
protein, as well as a DXD-like motif (ERD), conserved in
mammals, Drosophila, and C. elegans. Both features are
characteristic of several glycosyltransferase families.
The membrane-bound pre-protein is released by
proteolysis and, as for most glycosyltransferases, is
strongly activated by manganese. O-FucT-1 is similar to
family 1 glycosyltransferases (GT1).
Length = 347
Score = 26.0 bits (58), Expect = 2.0
Identities = 14/61 (22%), Positives = 20/61 (32%), Gaps = 14/61 (22%)
Query: 4 RGDASPRDIDTAMKLGAGYPMGPF------------ELADYVGHDTTKFIIDGWHKKFPE 51
ASP D MK G P GPF + + W+++FP
Sbjct: 97 SPRASPDSKDCPMK--EGNPFGPFWDHFGVDFDGSELYGPLSYDTFYPDVREAWNERFPP 154
Query: 52 N 52
+
Sbjct: 155 S 155
>gnl|CDD|227127 COG4789, EscV, Type III secretory pathway, component EscV
[Intracellular trafficking and secretion].
Length = 689
Score = 26.1 bits (58), Expect = 2.2
Identities = 10/47 (21%), Positives = 24/47 (51%), Gaps = 8/47 (17%)
Query: 30 ADYVGHDTTKFIIDGWHKKFPE--------NPLFKPVDALNKLVDEG 68
+++G T++++D +K+ + PL + + L +LV+E
Sbjct: 494 NEFIGIQETRYLLDQMERKYSDLVKEVQRQIPLQRIAEILQRLVEER 540
>gnl|CDD|218451 pfam05129, Elf1, Transcription elongation factor Elf1 like. This
family of short proteins contains a putative zinc
binding domain with four conserved cysteines. ELF1 has
been identified as a transcription elongation factor in
Saccharomyces cerevisiae.
Length = 74
Score = 25.3 bits (56), Expect = 2.4
Identities = 5/21 (23%), Positives = 10/21 (47%)
Query: 47 KKFPENPLFKPVDALNKLVDE 67
+ N L +P+D + +D
Sbjct: 51 FQTEINALSEPIDVYSDWIDA 71
>gnl|CDD|238682 cd01386, MYSc_type_XVIII, Myosin motor domain, type XVIII myosins.
This catalytic (head) domain has ATPase activity and
belongs to the larger group of P-loop NTPases. Myosins
are actin-dependent molecular motors that play important
roles in muscle contraction, cell motility, and
organelle transport. The head domain is a molecular
motor, which utilizes ATP hydrolysis to generate
directed movement toward the plus end along actin
filaments. A cyclical interaction between myosin and
actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle.
Length = 767
Score = 26.0 bits (57), Expect = 2.5
Identities = 11/60 (18%), Positives = 19/60 (31%), Gaps = 2/60 (3%)
Query: 9 PRDIDTAMKLGAGYPMGP--FELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVD 66
R+ GP F L +G + + + GW ++ NP L +
Sbjct: 497 DRETRETGLSRLRTCEGPLQFVLFHLLGTNPVLYDVTGWLRRAKPNPAALNAPQLLQDSK 556
>gnl|CDD|182464 PRK10441, PRK10441, iron-enterobactin transporter membrane protein;
Provisional.
Length = 335
Score = 25.4 bits (56), Expect = 3.2
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 62 NKLVDEGKLGVKSGEGF 78
N L D G LGV +G F
Sbjct: 87 NPLADPGLLGVNAGASF 103
>gnl|CDD|223739 COG0667, Tas, Predicted oxidoreductases (related to aryl-alcohol
dehydrogenases) [Energy production and conversion].
Length = 316
Score = 25.4 bits (56), Expect = 3.9
Identities = 13/30 (43%), Positives = 21/30 (70%), Gaps = 2/30 (6%)
Query: 42 IDGW--HKKFPENPLFKPVDALNKLVDEGK 69
ID + H+ PE P+ + ++AL++LV EGK
Sbjct: 120 IDLYQLHRPDPETPIEETLEALDELVREGK 149
>gnl|CDD|233396 TIGR01399, hrcV, type III secretion protein, HrcV family. Members
of this family are closely homologous to the flagellar
biosynthesis protein FlhA (TIGR01398) and should all
participate in type III secretion systems. Examples
include InvA (Salmonella enterica), LcrD (Yersinia
enterocolitica), HrcV (Xanthomonas), etc. Type III
secretion systems resemble flagellar biogenesis systems,
and may share the property of translocating special
classes of peptides through the membrane [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 677
Score = 25.4 bits (56), Expect = 3.9
Identities = 11/46 (23%), Positives = 24/46 (52%), Gaps = 8/46 (17%)
Query: 31 DYVGHDTTKFIIDGWHKKFPE--------NPLFKPVDALNKLVDEG 68
+++G T++++D +++PE PL + + L +LV E
Sbjct: 486 EFIGIQETRYLLDQMEREYPELVKEVQRVLPLQRIAEVLQRLVSEQ 531
>gnl|CDD|225428 COG2873, MET17, O-acetylhomoserine sulfhydrylase [Amino acid
transport and metabolism].
Length = 426
Score = 25.3 bits (56), Expect = 4.4
Identities = 10/25 (40%), Positives = 11/25 (44%), Gaps = 1/25 (4%)
Query: 18 LGAGYPMGPFEL-ADYVGHDTTKFI 41
Y P E AD V H TK+I
Sbjct: 186 FATPYLCRPIEHGADIVVHSATKYI 210
>gnl|CDD|130393 TIGR01326, OAH_OAS_sulfhy, OAH/OAS sulfhydrylase. This model
describes a distinct clade of the Cys/Met metabolism
pyridoxal phosphate-dependent enzyme superfamily.
Members include examples of OAH/OAS sulfhydrylase, an
enzyme with activity both as O-acetylhomoserine (OAH)
sulfhydrylase (EC 2.5.1.49) and O-acetylserine (OAS)
sulphydrylase (EC 2.5.1.47). An alternate name for OAH
sulfhydrylase is homocysteine synthase. This model is
designated subfamily because it may or may not have both
activities [Amino acid biosynthesis, Aspartate family,
Amino acid biosynthesis, Serine family].
Length = 418
Score = 25.0 bits (55), Expect = 5.1
Identities = 14/50 (28%), Positives = 18/50 (36%), Gaps = 17/50 (34%)
Query: 19 GAGYPMGPFEL-ADYVGHDTTKF-----------IIDG----WHK-KFPE 51
Y P + AD V H TK+ I+DG W +FP
Sbjct: 182 ATPYLCRPIDHGADIVVHSATKYIGGHGTAIGGVIVDGGKFDWANGRFPL 231
>gnl|CDD|181567 PRK08861, PRK08861, cystathionine gamma-synthase; Provisional.
Length = 388
Score = 24.9 bits (54), Expect = 5.5
Identities = 11/17 (64%), Positives = 13/17 (76%), Gaps = 1/17 (5%)
Query: 26 PFEL-ADYVGHDTTKFI 41
P EL AD+V H TTK+I
Sbjct: 185 PLELGADFVIHSTTKYI 201
>gnl|CDD|107029 PHA01351, PHA01351, putative minor structural protein.
Length = 1070
Score = 24.9 bits (54), Expect = 6.3
Identities = 7/9 (77%), Positives = 9/9 (100%)
Query: 50 PENPLFKPV 58
P+NPLF+PV
Sbjct: 319 PQNPLFRPV 327
>gnl|CDD|184798 PRK14704, PRK14704, anaerobic ribonucleoside triphosphate
reductase; Provisional.
Length = 618
Score = 24.8 bits (54), Expect = 6.3
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 14/40 (35%)
Query: 8 SPRDIDTAMKL--------------GAGYPMGPFELADYV 33
P+DI +A+ L G + + +LA YV
Sbjct: 109 QPQDIKSALALSSIIFQANQNMQHGGQSFALFDVDLAPYV 148
>gnl|CDD|234433 TIGR03992, Arch_glmU, UDP-N-acetylglucosamine
diphosphorylase/glucosamine-1-phosphate
N-acetyltransferase. The MJ_1101 protein from
Methanococcus jannaschii has been characterized as the
GlmU enzyme catalyzing the final two steps of UDP-GlcNAc
biosynthesis. Many of the genes identified by this model
are in proximity to the GlmS and GlmM genes and are also
presumed to be GlmU. However, some archaeal genomes
contain multiple closely-related homologs from this
family and it is not clear what the substrate
specificity is for each of them.
Length = 393
Score = 24.5 bits (54), Expect = 6.9
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 59 DALNKLVDEGKLGVKSGEGFYN 80
DAL L+DEGK+ +GF+
Sbjct: 191 DALQLLIDEGKVKAVELDGFWL 212
>gnl|CDD|150620 pfam09966, DUF2200, Uncharacterized protein conserved in bacteria
(DUF2200). This domain, found in various hypothetical
bacterial proteins, has no known function.
Length = 111
Score = 24.1 bits (53), Expect = 8.4
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 51 ENPLFKPVDALNKLVDE 67
E+PL + + L+KLVDE
Sbjct: 83 EDPLMQEIRYLDKLVDE 99
>gnl|CDD|233279 TIGR01125, TIGR01125, ribosomal protein S12 methylthiotransferase
RimO. Members of this protein are the
methylthiotransferase RimO, which modifies a conserved
Asp residue in ribosomal protein S12. This clade of
radical SAM family proteins is closely related to the
tRNA modification bifunctional enzyme MiaB (see
TIGR01574), and it catalyzes the same two types of
reactions: a radical-mechanism sulfur insertion, and a
methylation of the inserted sulfur. This clade spans
alpha and gamma proteobacteria, cyano bacteria,
Deinococcus, Porphyromonas, Aquifex, Helicobacter,
Campylobacter, Thermotoga, Chlamydia, Streptococcus
coelicolor and Clostridium, but does not include most
other gram positive bacteria, archaea or eukaryotes
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 430
Score = 24.3 bits (53), Expect = 9.3
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 18 LGAGYPMGP-FELADYVGHDTTKFIIDGWHKKFPENPLFKPVDALNKLVDEGKLGVKSGE 76
AGY + P +E ADYV +T FI D ++ + + + DA K++ G L + E
Sbjct: 24 REAGYEVTPNYEDADYVIVNTCGFIEDA--RQESIDTIGELADAGKKVIVTGCLVQRYKE 81
>gnl|CDD|99738 cd00614, CGS_like, CGS_like: Cystathionine gamma-synthase is a PLP
dependent enzyme and catalyzes the committed step of
methionine biosynthesis. This pathway is unique to
microorganisms and plants, rendering the enzyme an
attractive target for the development of antimicrobials
and herbicides. This subgroup also includes
cystathionine gamma-lyases (CGL), O-acetylhomoserine
sulfhydrylases and O-acetylhomoserine thiol lyases.
CGL's are very similar to CGS's. Members of this group
are widely distributed among all three forms of life.
Length = 369
Score = 24.1 bits (53), Expect = 9.8
Identities = 10/17 (58%), Positives = 11/17 (64%), Gaps = 1/17 (5%)
Query: 26 PFEL-ADYVGHDTTKFI 41
P EL AD V H TK+I
Sbjct: 172 PLELGADIVVHSATKYI 188
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
0.317 0.142 0.441
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,418,897
Number of extensions: 357578
Number of successful extensions: 422
Number of sequences better than 10.0: 1
Number of HSP's gapped: 406
Number of HSP's successfully gapped: 49
Length of query: 83
Length of database: 10,937,602
Length adjustment: 52
Effective length of query: 31
Effective length of database: 8,631,194
Effective search space: 267567014
Effective search space used: 267567014
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: 53 (24.2 bits)