RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781172|ref|YP_003065585.1| NAD-dependent DNA ligase LigA
[Candidatus Liberibacter asiaticus str. psy62]
(731 letters)
>gnl|CDD|30621 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type
II) [DNA replication, recombination, and repair].
Length = 667
Score = 682 bits (1762), Expect = 0.0
Identities = 284/711 (39%), Positives = 434/711 (61%), Gaps = 48/711 (6%)
Query: 11 ALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSED 70
A S+ +A++E+ L + ++ HD YY P + D+EYD L R + P+L
Sbjct: 1 AWSMAEAQEEIEELRELLNKHDYRYYVLDAPSVSDAEYDQLYRELQELEEKHPELIT--- 57
Query: 71 PNGPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTL 130
P+ P ++G + KV H +P LSL+ ++ E+LR F RI +F +S+ + +
Sbjct: 58 PDSPTQRVGAAPLNAFKKVRHPVPMLSLDNAFDEEELRAFDRRIRKFL----GDSVEYVV 113
Query: 131 EPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGE 190
EPKIDG I++ YE GK V AA RGDG +GED++A +R I +IP L P ++EVRGE
Sbjct: 114 EPKIDGLAISLVYENGKLVRAATRGDGTTGEDITANVRTIRSIPLKLP-GAPAVLEVRGE 172
Query: 191 VYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDIT-RYLNFFVHGLGKTSEI 249
V++ K DF ALN+E G KP+ANPRNAA+G LR+L+P R L FF++ +G E
Sbjct: 173 VFMPKEDFEALNEEREEEGEKPFANPRNAAAGSLRQLDPKITAKRKLGFFIYAVGDGEEG 232
Query: 250 -FAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDE 308
A Q E L ++ GFPVN R ++++Y E + R++LPYDIDG+V KV++
Sbjct: 233 LLADTQSERLAFLKAWGFPVNPYTRLCKNADEVLAFYEEWEKKRASLPYDIDGVVIKVND 292
Query: 309 FSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALI 368
+LQ++LG +++PRW I++KF ++A T+LLDI++Q+GRTG +TPVARLEPV + G +
Sbjct: 293 LALQRELGFTSKAPRWAIAYKFPAEEAVTKLLDIEVQVGRTGAITPVARLEPVELAGVTV 352
Query: 369 TNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPF 428
+ ATLHN D IK DIR+GD V+V++AG+VIP+VV +++ +R + +P
Sbjct: 353 SRATLHNVDEIKRK-----------DIRIGDTVVVRKAGDVIPQVVGVVLEKRPGNEKPI 401
Query: 429 SFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGK 488
FP+ CP+C S +VR + RCT GL C AQ ERL HFVSR+A +I+GLG+
Sbjct: 402 PFPTHCPVCGSELVR------EEGEVVIRCTNGLNCPAQLKERLIHFVSRNALDIDGLGE 455
Query: 489 QQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNI 548
+ ++ F+ I+ AD++TL + ++ GFG+ S NL ++I K +
Sbjct: 456 KIIEQLFEKG----LIKDIADLYTLTEED------LLSLEGFGEKSAENLLNAIEKSKKQ 505
Query: 549 SLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDII 608
L RF+++LGIRHVG A+SLA+++ + + ++A + ++ S +P +G+++
Sbjct: 506 PLARFLYALGIRHVGETTAKSLARHFGTLE-------ALLAASEEELAS---IPGIGEVV 555
Query: 609 AQAIVEFYQNPRNICAVEALLKE-VSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQ 667
A++I+EF+ N N ++ LL V +S + K V TGTL+ + R +A+
Sbjct: 556 ARSIIEFFANEENRELIDELLAAGVKWEEEEKISIETSPLAGKTFVLTGTLEGMSRDEAK 615
Query: 668 EYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLL 718
+ LGA VS +S+KTD ++ G+N GSKL KAQ+LGVKI++EE+FL LL
Sbjct: 616 ALLEALGAKVSGSVSKKTDYVVAGENAGSKLAKAQELGVKIIDEEEFLALL 666
>gnl|CDD|29013 cd00114, LIGANc, NAD+ dependent DNA ligase adenylation domain. DNA
ligases catalyze the crucial step of joining the breaks
in duplex DNA during DNA replication, repair and
recombination, utilizing either ATP or NAD(+) as a
cofactor, but using the same basic reaction mechanism.
The enzyme reacts with the cofactor to form a
phosphoamide-linked AMP with the amino group of a
conserved Lysine in the KXDG motif, and subsequently
transfers it to the DNA substrate to yield adenylated
DNA. This alignment contains members of the NAD+
dependent subfamily only..
Length = 307
Score = 315 bits (809), Expect = 2e-86
Identities = 130/313 (41%), Positives = 192/313 (61%), Gaps = 9/313 (2%)
Query: 19 KELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKI 78
+ ++ L + ++ HD YY +P + D+EYD L R A+ P+L P+ P ++
Sbjct: 1 ERIAELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELRALEEEHPELKT---PDSPTQRV 57
Query: 79 GGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTM 138
GG KV H +P LSL+ ++ E+LR F RI RF + +EPKIDG
Sbjct: 58 GGTPLSGFKKVRHPVPMLSLDNAFDEEELRAFDERIKRFL----GEEPAYVVEPKIDGLS 113
Query: 139 ITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDF 198
I++RYE G V AA RGDG +GEDV+ +R I +IP L+ PE +EVRGEV++ K DF
Sbjct: 114 ISLRYENGVLVQAATRGDGTTGEDVTENVRTIRSIPLTLA-GAPETLEVRGEVFMPKADF 172
Query: 199 LALNDEMIAVGRKPYANPRNAASGILRRLNPTDI-TRYLNFFVHGLGKTSEIFAKGQYEM 257
ALN E G KP+ANPRNAA+G LR+L+P R L FF++GLG+ + K Q E
Sbjct: 173 EALNKEREERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAEGLGPKTQSEA 232
Query: 258 LQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGE 317
L ++ GFPV+ R ++++Y+E+++ R +LPY+IDG+V KVD+ +LQ++LG
Sbjct: 233 LAFLKEWGFPVSPETRLCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDDLALQRELGF 292
Query: 318 RARSPRWMISHKF 330
+++PRW I++KF
Sbjct: 293 TSKAPRWAIAYKF 305
>gnl|CDD|145016 pfam01653, DNA_ligase_aden, NAD-dependent DNA ligase adenylation
domain. DNA ligases catalyse the crucial step of
joining the breaks in duplex DNA during DNA replication,
repair and recombination, utilising either ATP or NAD(+)
as a cofactor. This domain is the catalytic adenylation
domain. The NAD+ group is covalently attached to this
domain at the lysine in the KXDG motif of this domain.
This enzyme- adenylate intermediate is an important
feature of the proposed catalytic mechanism.
Length = 315
Score = 305 bits (783), Expect = 3e-83
Identities = 130/320 (40%), Positives = 193/320 (60%), Gaps = 12/320 (3%)
Query: 15 EQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGP 74
E+A++E++ L + I +D YY P + D+EYD L RR A+ FP+L P+ P
Sbjct: 1 EEAQQEIARLRELIRQYDYHYYVLDNPEVPDAEYDRLYRRLQALEEKFPELIT---PDSP 57
Query: 75 LNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKI 134
++G + KV H P LSL+ ++ ++L +I RI R + + +EPKI
Sbjct: 58 TQRVGAPLLGDFKKVRHPAPMLSLDNAFDEDELAAWIRRIRRRLGNSEKA---YVVEPKI 114
Query: 135 DGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYIS 194
DG +++ YE G V AA RGDG +GEDV+ ++ I IP L + P +EVRGEV++
Sbjct: 115 DGVAVSLTYEDGVLVRAATRGDGTTGEDVTQNVKTIRAIPLTLPGD-PARLEVRGEVFMP 173
Query: 195 KNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDIT--RYLNFFVHGLGKTSEIF-- 250
K DF ALN+E G KP+ANPRNAA+G LR+L+P +IT R L FFV+GLG +
Sbjct: 174 KEDFEALNEEREEEGEKPFANPRNAAAGSLRQLDP-EITAKRKLRFFVYGLGLPEGLELG 232
Query: 251 AKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFS 310
+ Q E L++++ LGFPV+ R ++ YY E + R LP++IDG+V KV+E
Sbjct: 233 PQTQSEALKQLKSLGFPVSPHTRLCKNIDEVLDYYAEWEKKRDELPFEIDGVVVKVNELP 292
Query: 311 LQKQLGERARSPRWMISHKF 330
LQ++LG +++PRW I++KF
Sbjct: 293 LQRELGFTSKAPRWAIAYKF 312
>gnl|CDD|145978 pfam03120, DNA_ligase_OB, NAD-dependent DNA ligase OB-fold domain.
DNA ligases catalyse the crucial step of joining the
breaks in duplex DNA during DNA replication, repair and
recombination, utilising either ATP or NAD(+) as a
cofactor. This family is a small domain found after the
adenylation domain pfam01653 in NAD dependent ligases.
OB-fold domains generally are involved in nucleic acid
binding.
Length = 82
Score = 118 bits (297), Expect = 7e-27
Identities = 45/93 (48%), Positives = 66/93 (70%), Gaps = 11/93 (11%)
Query: 335 ASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRD 394
A T+LLDI++Q+GRTG++TPVA LEPV + G ++ ATLHNED I+ D
Sbjct: 1 AVTKLLDIEVQVGRTGVITPVAILEPVELAGTTVSRATLHNEDEIEEK-----------D 49
Query: 395 IRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQP 427
IR+GD V+V++AG+VIPK+V +++ +R D +P
Sbjct: 50 IRIGDTVVVRKAGDVIPKIVGVVLEKRPGDTRP 82
>gnl|CDD|34872 COG5275, COG5275, BRCT domain type II [General function prediction
only].
Length = 276
Score = 69.4 bits (169), Expect = 4e-12
Identities = 31/89 (34%), Positives = 50/89 (56%), Gaps = 1/89 (1%)
Query: 631 EVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIV 690
+ + G + ++ K VFTG L+ + R A+ V G V+A+ S KT +++
Sbjct: 141 ATTQTPGSVPEGERECLKGKVFVFTGDLKTLSRDDAKTLVKVYGGRVTAVPSSKTTFLVL 200
Query: 691 GDNPG-SKLEKAQQLGVKIMNEEQFLFLL 718
GDN G SK+EK +QL +K ++EE F L+
Sbjct: 201 GDNAGPSKMEKIKQLKIKAIDEEGFDSLI 229
>gnl|CDD|28909 cd00027, BRCT, Breast Cancer Suppressor Protein (BRCA1),
carboxy-terminal domain. The BRCT domain is found within
many DNA damage repair and cell cycle checkpoint
proteins. The unique diversity of this domain
superfamily allows BRCT modules to interact forming
homo/hetero BRCT multimers, BRCT-non-BRCT interactions,
and interactions within DNA strand breaks..
Length = 72
Score = 54.6 bits (131), Expect = 1e-07
Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 649 NKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSK-LEKAQQLGVK 707
V TG L +R + +E + +LG V++ +S+KT +IVG + G K L KA +LG+
Sbjct: 1 GLTFVITGDLPSEERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKKLLKAIKLGIP 60
Query: 708 IMNEEQFLFLLQ 719
I+ E L L+
Sbjct: 61 IVTPEWLLDCLK 72
>gnl|CDD|144208 pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain. The BRCT domain
is found predominantly in proteins involved in cell
cycle checkpoint functions responsive to DNA damage. The
BRCT domain of XRCC1 forms a homodimer in the crystal
structure. This suggests that pairs of BRCT domains
associate as homo- or heterodimers. BRCT domains are
often found as tandem-repeat pairs. Structures of the
BRCA1 BRCT domains revealed a basis for a widely
utilized head-to-tail BRCT-BRCT oligomerisation mode.
This conserved tandem BRCT architecture facilitates
formation of the canonical BRCT phospho-peptide
interaction cleft at a groove between the BRCT domains.
Disease associated missense and nonsense mutations in
the BRCA1 BRCT domains disrupt peptide binding by
directly occluding this peptide binding groove, or by
disrupting key conserved BRCT core folding determinants.
Length = 77
Score = 52.8 bits (127), Expect = 4e-07
Identities = 29/72 (40%), Positives = 43/72 (59%), Gaps = 2/72 (2%)
Query: 648 ENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPG-SKLEKAQQLGV 706
+ K V TG L ++R + +E + +LG V+ LS+KT +IVG+N G KL KA LG+
Sbjct: 7 KGKTFVITG-LDSLEREELEELIEKLGGKVTDSLSKKTTHVIVGENAGTLKLLKAIALGI 65
Query: 707 KIMNEEQFLFLL 718
I+ EE L +
Sbjct: 66 PIVTEEWLLDCI 77
>gnl|CDD|37179 KOG1968, KOG1968, KOG1968, Replication factor C, subunit RFC1
(large subunit) [Replication, recombination and repair].
Length = 871
Score = 42.0 bits (98), Expect = 6e-04
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 650 KKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGS-KLEKAQQLGVKI 708
K TG L I A+ + + GA + LS KT +GD + KLEK ++L + +
Sbjct: 177 IKFTPTGVLDDIGTGSAEPSLKEFGASKTESLSDKTVESCLGDEAIAKKLEKIKELEIPV 236
Query: 709 MNEEQF 714
+ EE+
Sbjct: 237 LLEERK 242
>gnl|CDD|145977 pfam03119, DNA_ligase_ZBD, NAD-dependent DNA ligase C4 zinc finger
domain. DNA ligases catalyse the crucial step of
joining the breaks in duplex DNA during DNA replication,
repair and recombination, utilising either ATP or NAD(+)
as a cofactor. This family is a small zinc binding motif
that is presumably DNA binding. IT is found only in NAD
dependent DNA ligases.
Length = 27
Score = 36.3 bits (85), Expect = 0.031
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 7/34 (20%)
Query: 433 FCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSA 466
CP+C S +VR + G+ RCT G C A
Sbjct: 1 HCPVCGSPLVR----EEGE--VDIRCTNGS-CPA 27
>gnl|CDD|143896 pfam00122, E1-E2_ATPase, E1-E2 ATPase.
Length = 222
Score = 32.9 bits (76), Expect = 0.30
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 10/39 (25%)
Query: 387 KVMRGG-------RDIRVGDRVLVKRAGEVIPKVVDIIV 418
V+R G ++ VGD VL+K G+ +P D +
Sbjct: 37 TVIRDGKEEEIPADELVVGDIVLLK-PGDRVP--ADGRI 72
>gnl|CDD|31112 COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell
envelope biogenesis, outer membrane].
Length = 475
Score = 30.3 bits (68), Expect = 1.8
Identities = 29/89 (32%), Positives = 41/89 (46%), Gaps = 17/89 (19%)
Query: 352 LTPVA-RLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRV-------GDRVLV 403
L PV R+E VNIGG L+ HN D GL+ + + +R R+ GDR
Sbjct: 318 LKPVPGRMELVNIGGKLVIVDYAHNPD---GLEKALRAVRLHAAGRLIVVFGCGGDRDKS 374
Query: 404 KR--AGEVIPKVVDIIV----NERHPDAQ 426
KR G + ++ DI++ N R D
Sbjct: 375 KRPDMGAIAEQLADIVIVTSDNPRSEDPA 403
>gnl|CDD|35834 KOG0614, KOG0614, KOG0614, cGMP-dependent protein kinase [Signal
transduction mechanisms].
Length = 732
Score = 29.9 bits (67), Expect = 2.5
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 7/70 (10%)
Query: 84 LSLFKVTHSIPTLSLEKIWN-----IEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTM 138
L + K H + T E +++ +E FI R+YR + +D ++ +E + G +
Sbjct: 450 LKILKKKHIVDTKQQEHVFSERNIMMECRSDFIVRLYRTF--RDSKYVYMLMEACLGGEL 507
Query: 139 ITIRYEKGKF 148
TI ++G F
Sbjct: 508 WTILRDRGSF 517
>gnl|CDD|144965 pfam01565, FAD_binding_4, FAD binding domain. This family consists
of various enzymes that use FAD as a co-factor, most of
the enzymes are similar to oxygen oxidoreductase. One of
the enzymes Vanillyl-alcohol oxidase (VAO) has a solved
structure, the alignment includes the FAD binding site,
called the PP-loop, between residues 99-110. The FAD
molecule is covalently bound in the known structure,
however the residue that links to the FAD is not in the
alignment. VAO catalyses the oxidation of a wide variety
of substrates, ranging form aromatic amines to
4-alkylphenols. Other members of this family include
D-lactate dehydrogenase, this enzyme catalyses the
conversion of D-lactate to pyruvate using FAD as a
co-factor; mitomycin radical oxidase, this enzyme
oxidizes the reduced form of mitomycins and is involved
in mitomycin resistance. This family includes MurB an
UDP-N-acetylenolpyruvoylglucosamine reductase enzyme
EC:1.1.1.158. This enzyme is involved in the
biosynthesis of peptidoglycan.
Length = 138
Score = 29.9 bits (68), Expect = 2.6
Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 12/71 (16%)
Query: 334 QASTRLLDIDIQIGRTGILTPV--ARLEPVNIGGALITNATLHN-------EDYIKGL-- 382
+A L D+ + G+L + P +GGA+ TN + D + L
Sbjct: 68 EAGVTLGDLVRALAAKGLLLGLEPGSGIPGTVGGAIATNGGGYGSEKYGLTRDNVLSLEV 127
Query: 383 -DASGKVMRGG 392
A G+V+R
Sbjct: 128 VLADGEVVRLS 138
>gnl|CDD|144385 pfam00763, THF_DHG_CYH, Tetrahydrofolate
dehydrogenase/cyclohydrolase, catalytic domain.
Length = 117
Score = 29.4 bits (67), Expect = 3.3
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 14/56 (25%)
Query: 687 IIIVGDNPGS------KLEKAQQLGVK--------IMNEEQFLFLLQQYNTTLRIH 728
+I+VGD+P S K + A++LG++ + EE+ L L+++ N +H
Sbjct: 34 VILVGDDPASQVYVRSKRKAAEELGIESELIRLPEDITEEELLALIEKLNADPSVH 89
>gnl|CDD|33643 COG3853, TelA, Uncharacterized protein involved in tellurite
resistance [Inorganic ion transport and metabolism].
Length = 386
Score = 29.5 bits (66), Expect = 3.8
Identities = 20/114 (17%), Positives = 43/114 (37%), Gaps = 2/114 (1%)
Query: 567 ARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRN-ICAV 625
S+ + + YQ +I+ II + L R + +++ + E++++ I A
Sbjct: 129 KSSIQEIFSKYQTIGAQIDRIIESLSKGKDELTRDNKMLELLYEKNREYFEHLEKYIAAG 188
Query: 626 EALLKEVSPSIGRH-EKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS 678
E +E+ I + S + I R + + Y L +V+
Sbjct: 189 ELKDEELETEIIPELKTKAESGNQMDVQQVNELTLFINRLEQRVYDLLLARMVA 242
>gnl|CDD|32399 COG2217, ZntA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 713
Score = 29.0 bits (65), Expect = 4.2
Identities = 14/25 (56%), Positives = 18/25 (72%), Gaps = 3/25 (12%)
Query: 394 DIRVGDRVLVKRAGEVIPKVVDIIV 418
+++VGD VLV R GE IP VD +V
Sbjct: 229 EVQVGDIVLV-RPGERIP--VDGVV 250
>gnl|CDD|35773 KOG0553, KOG0553, KOG0553, TPR repeat-containing protein [General
function prediction only].
Length = 304
Score = 28.5 bits (63), Expect = 6.5
Identities = 12/98 (12%), Positives = 29/98 (29%), Gaps = 8/98 (8%)
Query: 640 EKNVSSEIENKKLVFTGTLQKIQRH---KAQEYVTQLGAVVSAILSRKTDIIIVGDNPGS 696
SE + L +Q ++ + + G + + P
Sbjct: 19 SFGWISEDGAESLEVA--IQCLEAAFGFRRDDVDRAEGTTLLDSFESAERHPVEILTPEE 76
Query: 697 KLEKAQQL---GVKIMNEEQFLFLLQQYNTTLRIHDDD 731
A+ L G K+M + + + +Y + + +
Sbjct: 77 DKALAESLKNEGNKLMKNKDYQEAVDKYTEAIELDPTN 114
>gnl|CDD|176179 cd05195, enoyl_red, enoyl reductase of polyketide synthase.
Putative enoyl reductase of polyketide synthase.
Polyketide synthases produce polyketides in step by step
mechanism that is similar to fatty acid synthesis. Enoyl
reductase reduces a double to single bond. Erythromycin
is one example of a polyketide generated by 3 complex
enzymes (megasynthases). 2-enoyl thioester reductase
(ETR) catalyzes the NADPH-dependent dependent conversion
of trans-2-enoyl acyl carrier protein/coenzyme A
(ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis.
2-enoyl thioester reductase activity has been linked in
Candida tropicalis as essential in maintaining
mitiochondrial respiratory function. This ETR family is
a part of the medium chain dehydrogenase/reductase
family, but lack the zinc coordination sites
characteristic of the alcohol dehydrogenases in this
family. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes or ketones. Alcohol dehydrogenase in the liver
converts ethanol and NAD+ to acetaldehyde and NADH,
while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains, at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding.
Length = 293
Score = 28.3 bits (64), Expect = 7.0
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 381 GLDASGKVMRGG---RDIRVGDRVLV 403
GL+ SG V R G ++VGDRV+
Sbjct: 32 GLECSGIVTRVGSGVTGLKVGDRVMG 57
>gnl|CDD|109652 pfam00604, Flu_PB2, Influenza RNA-dependent RNA polymerase subunit
PB2. PB2 can bind 5' end cap structure of RNA.
Length = 759
Score = 27.9 bits (62), Expect = 9.3
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 635 SIGRHE-KNVS-SEIENKKLVFTGTLQ--KIQRHKAQEYVTQLGAVVSAILSRKT 685
S G K +S S ++ ++ V G LQ KI+ + E T +G +AIL + T
Sbjct: 324 SFGGFTLKRISGSGVKREEEVLIGNLQTLKIRIWEGYEEFTMVGKRATAILRKAT 378
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
0.321 0.138 0.400
Gapped
Lambda K H
0.267 0.0779 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 8,965,741
Number of extensions: 496663
Number of successful extensions: 1246
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1223
Number of HSP's successfully gapped: 23
Length of query: 731
Length of database: 6,263,737
Length adjustment: 101
Effective length of query: 630
Effective length of database: 4,081,228
Effective search space: 2571173640
Effective search space used: 2571173640
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: 61 (27.2 bits)