RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780425|ref|YP_003064838.1| apolipoprotein
N-acyltransferase [Candidatus Liberibacter asiaticus str. psy62]
(518 letters)
>gnl|CDD|31157 COG0815, Lnt, Apolipoprotein N-acyltransferase [Cell envelope
biogenesis, outer membrane].
Length = 518
Score = 223 bits (570), Expect = 9e-59
Identities = 126/523 (24%), Positives = 241/523 (46%), Gaps = 26/523 (4%)
Query: 4 IAGKVMLLSGFRRCFIAILAGVIGSFSMPSSDLFLSSFVSFTLLIWLLDGISSNLGRMSA 63
+A + +L RR +A++ G + + + P D + ++ S L+WL+ G A
Sbjct: 5 LARQWVLGRPARRLLLALVFGALFALAFPPPDWWWLAWFSLAPLLWLVRG---------A 55
Query: 64 ISRVGSSFFVGWLFGVGYFLAGLWWVREGIVDQIGSRFPFWGVVLFFVMISFLLAIFYGV 123
+ G+LFG G+FLAG +W+ + G + L ++++ LA+F +
Sbjct: 56 PTSWEGLAKSGFLFGFGFFLAGFYWLGTSLGV--GLGLLAVALPLLVLLLAAWLALFLLL 113
Query: 124 ATSLASLLWSTGMGRICVFACAVGFCEWLRSVLGIG-TWNAIGYAAMPIPVMMQSVHWIG 182
L LW + + A EWLR G W +GY+ ++Q G
Sbjct: 114 VAVLTCRLWFALLVVPSAWVAA----EWLRGWSLTGFPWLLLGYSQWSPSPLLQLASLGG 169
Query: 183 LFGMNALSVFCFASPALFGTRRDVNIGIILSSTLLILHIAYGWWILTEDSKSSLKFEKIS 242
++ ++ L V A A +R ++L LL++ +AYG +L + ++
Sbjct: 170 VWLLSFLVVAVNALLASVLLKRATGGRLLLLGLLLVVLLAYGCALLGLAGSVPVGEPTLT 229
Query: 243 PVIRIVQPGINPAIK---EDREKILERYLSLTALPVSAGELEPVIIVWAYLPFPFSIVDQ 299
+ +VQ I +K + +++ YL L + +P ++VW PF +
Sbjct: 230 --VALVQGNIPQDLKWDADALARLIAGYLEEEFLAA-VDKQKPDLVVWPETALPFDLTRH 286
Query: 300 PSILKKIAS-VLKINQLLIVGSMRKELVDGRSHFYKSIYIINSKGEILASSNAKHLVPFA 358
P L ++A + ++ L++G+ G +Y S+ +++ GE + + HLVPF
Sbjct: 287 PDALARLAEALQRVGAPLLIGTDVDGPAPGGGIYYNSVLVLDPGGEGVYRYDKVHLVPFG 346
Query: 359 EYLPYRNILKKLNLDFYMFPLDYSSSDISPLLGLSEKLRLYPLLFSDALFHQDI--NNLE 416
EY+P+ +L+ L + D+S +L L+ ++ PL+ +A+F + + + +
Sbjct: 347 EYIPFPELLRPLYFFLNLPMSDFSRGPGPQVLLLAGGPKIAPLICYEAIFPELVRASARQ 406
Query: 417 NVSAILNIIDDSGFMGS-GTDHSFRYAQIQAVEIGLPLIRATNNGVSAFLDERGQIISSV 475
+LN+ +D+ F GS G F+ A+++AVE+G PL+RATN G+SA +D RG+I++ +
Sbjct: 407 GAELLLNLSNDAWFGGSWGPYQHFQQARVRAVELGRPLVRATNTGISAVIDPRGRILAQL 466
Query: 476 YADRGASIDMHFQPKVRDSFRSSIQMRVFWIIEFILLILAVIV 518
+D K + + W++ + L A++
Sbjct: 467 PYFTRGVLDATVPLKTGLTPYARWGDWPLWLLVGLALAAALLF 509
>gnl|CDD|143595 cd07571, ALP_N-acyl_transferase, Apolipoprotein N-acyl transferase
(class 9 nitrilases). ALP N-acyl transferase (Lnt), is
an essential membrane-bound enzyme in gram-negative
bacteria, which catalyzes the N-acylation of
apolipoproteins, the final step in lipoprotein
maturation. This is a reverse amidase (i.e.
condensation) reaction. This subgroup belongs to a
larger nitrilase superfamily comprised of nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes,
which depend on a Glu-Lys-Cys catalytic triad. This
superfamily has been classified in the literature based
on global and structure based sequence analysis into
thirteen different enzyme classes (referred to as 1-13),
this subgroup corresponds to class 9.
Length = 270
Score = 137 bits (347), Expect = 9e-33
Identities = 73/258 (28%), Positives = 120/258 (46%), Gaps = 24/258 (9%)
Query: 245 IRIVQPGINPAIK---EDREKILERYLSLTALPVSAGELEPVIIVWAYLP---FPFSIVD 298
+ +VQ I K E R+ L+RYL LT P ++VW P PF +
Sbjct: 3 VALVQGNIPQDEKWDPEQRQATLDRYLDLTRELADEK---PDLVVW---PETALPFDLQR 56
Query: 299 QPSILKKIASVLK-INQLLIVGSMRKELVDGRSHFYKSIYIINSKGEILASSNAKHLVPF 357
P L ++A + + L+ G+ R+E G +Y S +++ G IL + HLVPF
Sbjct: 57 DPDALARLARAARAVGAPLLTGAPRRE--PGGGRYYNSALLLDPGGGILGRYDKHHLVPF 114
Query: 358 AEYLPYRNILKKLNLDFYMFPLDYSSSDISPLLGLSEKLRLYPL-----LFSDALFHQDI 412
EY+P R++L+ L L F + D+S L L +R+ PL +F + +
Sbjct: 115 GEYVPLRDLLRFLGLLFDLPMGDFSPGTGPQPLLLGGGVRVGPLICYESIFPELVRDAV- 173
Query: 413 NNLENVSAILNIIDDSGFMGS-GTDHSFRYAQIQAVEIGLPLIRATNNGVSAFLDERGQI 471
+ ++NI +D+ F S G A+++A+E G PL+RA N G+SA +D G+I
Sbjct: 174 --RQGADLLVNITNDAWFGDSAGPYQHLAMARLRAIETGRPLVRAANTGISAVIDPDGRI 231
Query: 472 ISSVYADRGASIDMHFQP 489
++ + +
Sbjct: 232 VARLPLFEAGVLVAEVPL 249
>gnl|CDD|144405 pfam00795, CN_hydrolase, Carbon-nitrogen hydrolase. This family
contains hydrolases that break carbon-nitrogen bonds.
The family includes: Nitrilase EC:3.5.5.1, Aliphatic
amidase EC:3.5.1.4, Biotidinase EC:3.5.1.12,
Beta-ureidopropionase EC:3.5.1.6. Nitrilase-related
proteins generally have a conserved E-K-C catalytic
triad, and are multimeric alpha-beta-beta-alpha sandwich
proteins.
Length = 172
Score = 35.4 bits (82), Expect = 0.040
Identities = 29/145 (20%), Positives = 55/145 (37%), Gaps = 15/145 (10%)
Query: 245 IRIVQPGINPAIKEDREKILERYLSLTALPVSAG-------ELEPVIIVWAYLPFPFSIV 297
+ +VQ + P+ D E L++ L L G EL +
Sbjct: 2 VALVQ--LPPS-AFDLEANLQKLLELIEEAARQGADLIVFPELFIPGYAHGAAEYLELAE 58
Query: 298 DQPSI-LKKIASVLKINQLLIVGSMRKELVDGRSHFYKSIYIINSKGEILASSNAKHLVP 356
P L+ ++++ + N + +V + Y ++ +I+ GE+L +HLVP
Sbjct: 59 AIPGEVLQALSALARKNGITVVAGI---PERDGGGLYNTLVLIDPDGELLGKYRKRHLVP 115
Query: 357 FAEYLPYRNILKKLNLDFYMFPLDY 381
F E++ R + F +F
Sbjct: 116 FGEWVE-RPLFGPGGATFPVFDTPV 139
>gnl|CDD|143587 cd07197, nitrilase, Nitrilase superfamily, including nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes.
This superfamily (also known as the C-N hydrolase
superfamily) contains hydrolases that break
carbon-nitrogen bonds; it includes nitrilases, cyanide
dihydratases, aliphatic amidases, N-terminal amidases,
beta-ureidopropionases, biotinidases, pantotheinase,
N-carbamyl-D-amino acid amidohydrolases, the glutaminase
domain of glutamine-dependent NAD+ synthetase,
apolipoprotein N-acyltransferases, and
N-carbamoylputrescine amidohydrolases, among others.
These enzymes depend on a Glu-Lys-Cys catalytic triad,
and work through a thiol acylenzyme intermediate.
Members of this superfamily generally form homomeric
complexes, the basic building block of which is a
homodimer. These oligomers include dimers, tetramers,
hexamers, octamers, tetradecamers, octadecamers, as well
as variable length helical arrangements and
homo-oligomeric spirals. These proteins have roles in
vitamin and co-enzyme metabolism, in detoxifying small
molecules, in the synthesis of signaling molecules, and
in the post-translational modification of proteins. They
are used industrially, as biocatalysts in the fine
chemical and pharmaceutical industry, in cyanide
remediation, and in the treatment of toxic effluent.
This superfamily has been classified previously in the
literature, based on global and structure-based sequence
analysis, into thirteen different enzyme classes
(referred to as 1-13). This hierarchy includes those
thirteen classes and a few additional subfamilies. A
putative distant relative, the plasmid-borne TraB
family, has not been included in the hierarchy.
Length = 253
Score = 33.5 bits (77), Expect = 0.15
Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 6/57 (10%)
Query: 303 LKKIASVLKINQLLIVGSMRKELVDGRSHFYKSIYIINSKGEILASSNAKHLVPFAE 359
L ++A L I ++ G K Y + +I+ GEI+ HL F E
Sbjct: 68 LAELAKELGIY--IVAGIAEK----DGDKLYNTAVVIDPDGEIIGKYRKIHLFDFGE 118
>gnl|CDD|144721 pfam01231, IDO, Indoleamine 2,3-dioxygenase.
Length = 407
Score = 32.6 bits (75), Expect = 0.29
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 11/54 (20%)
Query: 388 PLLGLSEKLRLYPLLFSDAL--------FHQDINNLENVSAILNI---IDDSGF 430
PLL +SE L L P+L L D +L+N+S I D+S F
Sbjct: 104 PLLEVSEHLGLPPILTYADLVLWNWKPIDPDDPLDLDNLSTINTFTGTKDESWF 157
>gnl|CDD|143898 pfam00124, Photo_RC, Photosynthetic reaction centre protein.
Length = 257
Score = 31.0 bits (71), Expect = 0.74
Identities = 33/109 (30%), Positives = 45/109 (41%), Gaps = 18/109 (16%)
Query: 71 FFVGWLFGVGYFLAGLWWVREGIVDQIGSRFPFWGVVLFFVMISFLLAIF-----YGVAT 125
F+VGW FGV + G I+ + W +LF F LA+ YG+
Sbjct: 1 FYVGW-FGVLSIIFGALGAF--IIGFNAAASVTWNPLLFGRNF-FWLAVEPPSAEYGL-- 54
Query: 126 SLASLLWSTGMGRICVFACAVGFCEW-LRSV-----LGIGTWNAIGYAA 168
S A LW G+ +I F F W LR LG+G A ++A
Sbjct: 55 SFA-PLWEGGLWQIITFFATGAFLSWWLREYEIARKLGMGPHVAWAFSA 102
>gnl|CDD|143607 cd07583, nitrilase_5, Uncharacterized subgroup of the nitrilase
superfamily (putative class 13 nitrilases). The
nitrilase superfamily is comprised of nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes,
which depend on a Glu-Lys-Cys catalytic triad. This
superfamily has been classified in the literature based
on global and structure based sequence analysis into
thirteen different enzyme classes (referred to as 1-13).
Class 13 represents proteins that at the time were
difficult to place in a distinct similarity group; this
subgroup represents either a new class or one that was
included previously in class 13. Members of this
superfamily generally form homomeric complexes, the
basic building block of which is a homodimer.
Length = 253
Score = 30.2 bits (69), Expect = 1.6
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 5/58 (8%)
Query: 301 SILKKIASVLKINQLLIVGSMRKELVDGRSHFYKSIYIINSKGEILASSNAKHLVPFA 358
S L ++A +N ++ GS+ E G Y + Y+I+ GE++A+ HL
Sbjct: 64 SFLSELAKKHGVN--IVAGSV-AEKEGG--KLYNTAYVIDPDGELIATYRKIHLFGLM 116
>gnl|CDD|38864 KOG3660, KOG3660, KOG3660, Sodium-neurotransmitter symporter
[Signal transduction mechanisms].
Length = 629
Score = 29.9 bits (67), Expect = 1.6
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 8/67 (11%)
Query: 63 AISRVGSSFFVGWLFGVGYFLAGL---WWVREGIVDQIGSRFP-----FWGVVLFFVMIS 114
A++++ S LF L GL + + E IV I FP W VVLF ++
Sbjct: 374 ALAQMPLSPLWSGLFFFMLLLLGLDSQFAIVETIVTAIVDEFPRLRNRRWIVVLFVCVVG 433
Query: 115 FLLAIFY 121
FLL +
Sbjct: 434 FLLGLPL 440
>gnl|CDD|143643 cd07883, RHD-n_NFkB, N-terminal sub-domain of the Rel homology
domain (RHD) of nuclear factor of kappa light
polypeptide gene enhancer in B-cells (NF-kappa B).
Proteins containing the Rel homology domain (RHD) are
metazoan transcription factors. The RHD is composed of
two structural sub-domains; this model characterizes the
N-terminal RHD sub-domain of the NF-kappa B1 and B2
families of transcription factors, also referred to as
class I members of the NF-kappa B family. In class I
NF-kappa Bs, the RHD domain co-occurs with C-terminal
ankyrin repeats. Family members include NF-kappa B1 and
NF-kappa B2. NF-kappa B1 is commonly referred to as p105
or p50 (proteolytically processed form), while NF-kappa
B2 is called p100 or p52 (proteolytically processed
form). NF-kappa B proteins are part of a protein complex
that acts as a transcription factor, which is
responsible for regulating a host of cellular responses
to a variety of stimuli. This complex tightly regulates
the expression of a large number of genes, and is
involved in processes such as adaptive and innate
immunity, stress response, inflammation, cell adhesion,
proliferation and apoptosis. The cytosolic NF-kappa B
complex is activated via phosphorylation of the
ankyrin-repeat containing inhibitory protein I-kappa B,
which dissociates from the complex and exposes the
nuclear localization signal of the heterodimer (NF-kappa
B and REL). p105 and p100 may also act as I-kappa Bs due
to their C-terminal ankyrin repeats.
Length = 197
Score = 29.8 bits (67), Expect = 2.2
Identities = 13/26 (50%), Positives = 14/26 (53%)
Query: 7 KVMLLSGFRRCFIAILAGVIGSFSMP 32
K M LS R CF A L GSF+ P
Sbjct: 159 KSMDLSVVRLCFQAFLPDSNGSFTRP 184
>gnl|CDD|146370 pfam03699, UPF0182, Uncharacterized protein family (UPF0182). This
family contains uncharacterized integral membrane
proteins.
Length = 771
Score = 27.5 bits (62), Expect = 9.5
Identities = 19/83 (22%), Positives = 28/83 (33%), Gaps = 15/83 (18%)
Query: 64 ISRVGSSFFVGWLFGVGYFLAGLWWVREGIVDQIGSRFPFWGVV------------LFFV 111
++R+G V +F + FL L R S F + L +
Sbjct: 46 LTRIGLFLLVFLIFFLFLFLNLLLAYRARPPFVPLSPEQFGDPLARYRSVILPRRRLLLL 105
Query: 112 MISFLLAIFYGVATSLASLLWST 134
IS +L + G AS W T
Sbjct: 106 GISLVLGLLAG---LSASSRWET 125
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.328 0.143 0.438
Gapped
Lambda K H
0.267 0.0746 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 6,568,865
Number of extensions: 379065
Number of successful extensions: 1609
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1563
Number of HSP's successfully gapped: 164
Length of query: 518
Length of database: 6,263,737
Length adjustment: 98
Effective length of query: 420
Effective length of database: 4,146,055
Effective search space: 1741343100
Effective search space used: 1741343100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 60 (26.9 bits)