RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781223|ref|YP_003065636.1| intrrupted gp229, phage associated protein [Candidatus Liberibacter asiaticus str. psy62] (110 letters) >gnl|CDD|31246 COG1044, LpxD, UDP-3-O-[3-hydroxymyristoyl]. Length = 338 Score = 41.4 bits (97), Expect = 6e-05 Identities = 17/93 (18%), Positives = 31/93 (33%) Query: 8 RDCATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIV 67 A + A + A + N + N + +G + A +G N + Sbjct: 91 LFYRPFNPAAGIHPTAVIDPTATIGKNVSIGPNVVIGAGVVIGENVVIGAGAVIGENVKI 150 Query: 68 RDTAEVGGDAFVIGFTVISGNARVRGNAVVGGD 100 D + + + VI N + AV+G D Sbjct: 151 GDGTVIHPNVTIYHNVVIGNNVIIHSGAVIGAD 183 Score = 29.1 bits (65), Expect = 0.26 Identities = 12/69 (17%), Positives = 28/69 (40%) Query: 41 TYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGD 100 + A + A + N S+G N ++ +G + + VI N ++ V+ + Sbjct: 100 AGIHPTAVIDPTATIGKNVSIGPNVVIGAGVVIGENVVIGAGAVIGENVKIGDGTVIHPN 159 Query: 101 TVVEGDTVL 109 + + V+ Sbjct: 160 VTIYHNVVI 168 Score = 26.8 bits (59), Expect = 1.3 Identities = 12/90 (13%), Positives = 33/90 (36%), Gaps = 1/90 (1%) Query: 10 CATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRD 69 T ID + + + ++ + ++ N + ++ + G ++G+ +G I+ Sbjct: 213 ANTTIDRGAL-DDTVIGEGVKIDNLVQIGHNVRIGEHCIIAGQVGIAGSVKIGKYVIIGG 271 Query: 70 TAEVGGDAFVIGFTVISGNARVRGNAVVGG 99 + G + I + V + G Sbjct: 272 QVGIAGHLEIGDGVTIGARSGVMASITEPG 301 >gnl|CDD|32354 COG2171, DapD, Tetrahydrodipicolinate N-succinyltransferase [Amino acid transport and metabolism]. Length = 271 Score = 36.4 bits (84), Expect = 0.002 Identities = 27/107 (25%), Positives = 40/107 (37%), Gaps = 8/107 (7%) Query: 12 TVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTA 71 V + R+ A V A + V ++V A G V G ASVG A V + Sbjct: 104 FVPEGVRIVPGAIVRLGAYIAKGTVVMPESFVNIGAGTGEGTMVDGRASVGSCAQVGKNS 163 Query: 72 EVGGDAFVIGF--------TVISGNARVRGNAVVGGDTVVEGDTVLE 110 +GG A + G +I N + N+ V +V V+ Sbjct: 164 HIGGGASIGGVLEPLQANPVIIGDNCLIGANSEVVEGVIVGDGCVVA 210 Score = 28.7 bits (64), Expect = 0.38 Identities = 28/113 (24%), Positives = 38/113 (33%), Gaps = 14/113 (12%) Query: 3 DNAVVRDCATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASVG 62 A+VR A + V + V A + T V A VG A+V N+ +G Sbjct: 113 PGAIVRLGAYIAK------GTVVMPESFVNIGAGTGEGTMVDGRASVGSCAQVGKNSHIG 166 Query: 63 GNAIVRDTAEVG-------GDAFVIGFTVISGNA-RVRGNAVVGGDTVVEGDT 107 G A + E GD +IG V VV + DT Sbjct: 167 GGASIGGVLEPLQANPVIIGDNCLIGANSEVVEGVIVGDGCVVAAGVFITQDT 219 >gnl|CDD|34410 COG4801, COG4801, Predicted acyltransferase [General function prediction only]. Length = 277 Score = 35.3 bits (81), Expect = 0.004 Identities = 22/110 (20%), Positives = 43/110 (39%), Gaps = 5/110 (4%) Query: 3 DNAVVRDCATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVR-----DNAKVGGYAKVSG 57 N V + V+ + G S+ ++ V V + + + ++ + KV+G Sbjct: 8 PNTRVEEAIIVVKGDVIIGKNSMLKYGVVGEEIIVGERVRIYGDIVAKDIRIDMWCKVTG 67 Query: 58 NASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVVEGDT 107 N V +A + + + + G VIG I + + G V G V+ Sbjct: 68 NVIVENDAYIGEFSSIKGKLTVIGDLDIGADVIIEGGFVAKGWIVIRNPV 117 >gnl|CDD|100038 cd00208, LbetaH, Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity, however, some subfamilies in this hierarchy also show activities related to ion transport or translation initiation. Many are trimeric in their active forms.. Length = 78 Score = 34.5 bits (80), Expect = 0.006 Identities = 14/77 (18%), Positives = 28/77 (36%), Gaps = 2/77 (2%) Query: 29 AQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAE--VGGDAFVIGFTVIS 86 + ++ +R +G + A +G + +G + + VI Sbjct: 1 VFIGEGVKIHPKAVIRGPVVIGDNVNIGPGAVIGAATGPNEKNPTIIGDNVEIGANAVIH 60 Query: 87 GNARVRGNAVVGGDTVV 103 G ++ NAV+G VV Sbjct: 61 GGVKIGDNAVIGAGAVV 77 Score = 31.5 bits (72), Expect = 0.060 Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 8/71 (11%) Query: 47 AKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGF--------TVISGNARVRGNAVVG 98 +G K+ A + G ++ D +G A + T+I N + NAV+ Sbjct: 1 VFIGEGVKIHPKAVIRGPVVIGDNVNIGPGAVIGAATGPNEKNPTIIGDNVEIGANAVIH 60 Query: 99 GDTVVEGDTVL 109 G + + V+ Sbjct: 61 GGVKIGDNAVI 71 Score = 30.3 bits (69), Expect = 0.13 Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 4/64 (6%) Query: 4 NAVVRDCATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASVGG 63 AV+R + D+ + A + T + DN ++G A + G +G Sbjct: 12 KAVIRGPVVIGDNVNIGPGAVIGAATGPNEKNP----TIIGDNVEIGANAVIHGGVKIGD 67 Query: 64 NAIV 67 NA++ Sbjct: 68 NAVI 71 >gnl|CDD|100039 cd00710, LbH_gamma_CA, Gamma carbonic anhydrases (CA): Carbonic anhydrases are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism, involving the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three distinct groups of carbonic anhydrases - alpha, beta and gamma - which show no significant sequence identity or structural similarity. Gamma CAs are homotrimeric enzymes, with each subunit containing a left-handed parallel beta helix (LbH) structural domain.. Length = 167 Score = 33.4 bits (77), Expect = 0.015 Identities = 33/113 (29%), Positives = 52/113 (46%), Gaps = 9/113 (7%) Query: 4 NAVVRDCATVIDDARVSGNASVSRFAQVKSNA----EVSDNTYVRDN----AKVGGYAKV 55 +A V A VI D + N V A ++++ + N ++D A G + Sbjct: 8 SAYVHPTAVVIGDVIIGDNVFVGPGASIRADEGTPIIIGANVNIQDGVVIHALEGYSVWI 67 Query: 56 SGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVVEGDTV 108 N S+ AIV A +G + F IGF + NA+V N V+G + VV+G + Sbjct: 68 GKNVSIAHGAIVHGPAYIGDNCF-IGFRSVVFNAKVGDNCVIGHNAVVDGVEI 119 >gnl|CDD|31007 COG0663, PaaY, Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]. Length = 176 Score = 33.2 bits (76), Expect = 0.016 Identities = 21/115 (18%), Positives = 44/115 (38%), Gaps = 8/115 (6%) Query: 3 DNAVVRDCATVIDDARVSGNASVSRFAQVKSNAE---VSDNTYVRDNAKVGGYAK----V 55 A V ATVI D R+ S+ A ++ + E + T ++D + + Sbjct: 16 PTAFVAPSATVIGDVRIGAGVSIWPGAVLRGDVEPIRIGARTNIQDGVVIHADPGYPVTI 75 Query: 56 SGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVVEGDTVLE 110 + ++G A+V +G + + + A + ++VG +V + Sbjct: 76 GDDVTIGHGAVVH-GCTIGDNVLIGMGATVLDGAVIGDGSIVGAGALVTPGKEIP 129 >gnl|CDD|100060 cd05636, LbH_G1P_TT_C_like, Putative glucose-1-phosphate thymidylyltransferase, C-terminal Left-handed parallel beta-Helix (LbH) domain: Proteins in this family show simlarity to glucose-1-phosphate adenylyltransferases in that they contain N-terminal catalytic domains that resemble a dinucleotide-binding Rossmann fold and C-terminal LbH fold domains. Members in this family are predicted to be glucose-1-phosphate thymidylyltransferases, which are involved in the dTDP-L-rhamnose biosynthetic pathway. Glucose-1-phosphate thymidylyltransferase catalyzes the synthesis of deoxy-thymidine di-phosphate (dTDP)-L-rhamnose, an important component of the cell wall of many microorganisms. The C-terminal LbH domain contains multiple turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity.. Length = 163 Score = 32.6 bits (75), Expect = 0.025 Identities = 18/58 (31%), Positives = 24/58 (41%) Query: 46 NAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVV 103 V + G +G AIVR A + G + I NA +RG V+G VV Sbjct: 5 EGTVEEGVTIKGPVWIGEGAIVRSGAYIEGPVIIGKGCEIGPNAYIRGYTVLGDGCVV 62 Score = 28.7 bits (65), Expect = 0.40 Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 1/64 (1%) Query: 33 SNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVR 92 V + ++ +G A V A + G I+ E+G +A++ G+TV+ V Sbjct: 4 IEGTVEEGVTIKGPVWIGEGAIVRSGAYIEGPVIIGKGCEIGPNAYIRGYTVLGDGCVV- 62 Query: 93 GNAV 96 GN+V Sbjct: 63 GNSV 66 >gnl|CDD|36673 KOG1460, KOG1460, KOG1460, GDP-mannose pyrophosphorylase [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones]. Length = 407 Score = 31.8 bits (72), Expect = 0.041 Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 7/65 (10%) Query: 33 SNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVR 92 + AE+ + Y+ +AKV AK+ N S+G N V G + ++I +A + Sbjct: 281 TQAEIIGDVYIHPSAKVHPTAKIGPNVSIGANVRV-------GPGVRLRESIILDDAEIE 333 Query: 93 GNAVV 97 NAVV Sbjct: 334 ENAVV 338 >gnl|CDD|31400 COG1207, GlmU, N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]. Length = 460 Score = 31.7 bits (72), Expect = 0.046 Identities = 23/127 (18%), Positives = 52/127 (40%), Gaps = 24/127 (18%) Query: 3 DNAVVRDCATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRD-----NAKVGGYAKVS- 56 DNAV++ +VI+ + V A+V FA+++ A + + ++ + A +G +K Sbjct: 308 DNAVIKA-YSVIEGSTVGEGATVGPFARLRPGAVLGADVHIGNFVEVKKATIGKGSKAGH 366 Query: 57 ----GNASVGGNAIV-------------RDTAEVGGDAFVIGFTVISGNARVRGNAVVGG 99 G+A +G N + + +G + F+ + + + A + Sbjct: 367 LTYLGDAEIGENVNIGAGTITCNYDGKNKFKTIIGDNVFIGSNSQLVAPVTIGDGATIAA 426 Query: 100 DTVVEGD 106 + + D Sbjct: 427 GSTITKD 433 Score = 24.4 bits (53), Expect = 6.4 Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 6/44 (13%) Query: 67 VRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVVEGDTVLE 110 +R E+G D VI N + GN V+G + V+ +V++ Sbjct: 265 IRGDVEIGRD------VVIEPNVILEGNTVIGDNVVIGPGSVIK 302 Score = 24.0 bits (52), Expect = 9.8 Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 7/70 (10%) Query: 39 DNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVG 98 TY+R + ++G + N + GN ++ GD VIG + ++ + NAV+ Sbjct: 261 ATTYIRGDVEIGRDVVIEPNVILEGNTVI-------GDNVVIGPGSVIKDSVIGDNAVIK 313 Query: 99 GDTVVEGDTV 108 +V+EG TV Sbjct: 314 AYSVIEGSTV 323 >gnl|CDD|31245 COG1043, LpxA, Acyl-[acyl carrier protein]. Length = 260 Score = 31.3 bits (71), Expect = 0.053 Identities = 15/45 (33%), Positives = 22/45 (48%) Query: 65 AIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVVEGDTVL 109 AI+ AE+G D + F +I N + V+ VVEG T + Sbjct: 10 AIIEPGAEIGEDVKIGPFCIIGPNVEIGDGTVLKSHVVVEGHTTI 54 Score = 29.0 bits (65), Expect = 0.27 Identities = 15/58 (25%), Positives = 24/58 (41%) Query: 43 VRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGD 100 + A++G K+ +G N + D + V G T I N R+ A +G D Sbjct: 12 IEPGAEIGEDVKIGPFCIIGPNVEIGDGTVLKSHVVVEGHTTIGRNNRIFPFASIGED 69 Score = 29.0 bits (65), Expect = 0.28 Identities = 17/61 (27%), Positives = 30/61 (49%) Query: 40 NTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGG 99 +V + +G ++ NA++ G+ V D A +GG + V F I +A + G + V Sbjct: 118 YAHVAHDCVIGNNCILANNATLAGHVEVGDYAIIGGLSAVHQFVRIGAHAMIGGLSAVSQ 177 Query: 100 D 100 D Sbjct: 178 D 178 >gnl|CDD|31247 COG1045, CysE, Serine acetyltransferase [Amino acid transport and metabolism]. Length = 194 Score = 29.5 bits (66), Expect = 0.20 Identities = 15/67 (22%), Positives = 28/67 (41%), Gaps = 4/67 (5%) Query: 31 VKSNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNAR 90 + A + D+ + +GG K SG + + +G A ++G I NA+ Sbjct: 90 IGETAVIGDDVTIYHGVTLGGTGKESGKRHP----TIGNGVYIGAGAKILGNIEIGDNAK 145 Query: 91 VRGNAVV 97 + +VV Sbjct: 146 IGAGSVV 152 Score = 24.5 bits (53), Expect = 7.8 Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 2/50 (4%) Query: 32 KSNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIG 81 K + + + Y+ AK+ G ++ NA +G ++V +V +A V+G Sbjct: 117 KRHPTIGNGVYIGAGAKILGNIEIGDNAKIGAGSVV--LKDVPPNATVVG 164 >gnl|CDD|100041 cd03350, LbH_THP_succinylT, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA. It is the committed step in the succinylase pathway by which bacteria synthesize L-lysine and meso-diaminopimelate, a component of peptidoglycan. The enzyme is homotrimeric and each subunit contains an N-terminal region with alpha helices and hairpin loops, as well as a C-terminal region with a left-handed parallel alpha-helix (LbH) structural motif encoded by hexapeptide repeat motifs.. Length = 139 Score = 29.3 bits (66), Expect = 0.24 Identities = 25/112 (22%), Positives = 39/112 (34%), Gaps = 8/112 (7%) Query: 4 NAVVRDCATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKV------SG 57 V A + D A + A + + V A V + T V A VG A++ S Sbjct: 1 GRRVPPGAIIRDGAFIGPGAVLMMPSYVNIGAYVDEGTMVDSWATVGSCAQIGKNVHLSA 60 Query: 58 NASVGG--NAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVVEGDT 107 A +GG + + D F+ + V AV+ V+ T Sbjct: 61 GAVIGGVLEPLQATPVIIEDDVFIGANCEVVEGVIVGKGAVLAAGVVLTQST 112 >gnl|CDD|31401 COG1208, GCD1, Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure and biogenesis]. Length = 358 Score = 29.2 bits (65), Expect = 0.26 Identities = 10/36 (27%), Positives = 18/36 (50%) Query: 75 GDAFVIGFTVISGNARVRGNAVVGGDTVVEGDTVLE 110 A++IG VI A++ A++G TV+ + Sbjct: 254 RSAYIIGPVVIGPGAKIGPGALIGPYTVIGEGVTIG 289 >gnl|CDD|100058 cd04745, LbH_paaY_like, paaY-like: This group is composed by uncharacterized proteins with similarity to the protein product of the E. coli paaY gene, which is part of the paa gene cluster responsible for phenylacetic acid degradation. Proteins in this group are expected to adopt the left-handed parallel beta-helix (LbH) structure. They contain imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Similarity to gamma carbonic anhydrase and Ferripyochelin Binding Protein (FBP) may suggest metal binding capacity.. Length = 155 Score = 29.3 bits (66), Expect = 0.27 Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 5/64 (7%) Query: 41 TYVRDNAKVGGYAKVSG-----NASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNA 95 T + +N +G A + G NA VG NA+V D A +G ++ V + + + Sbjct: 62 TVLEENGHIGHGAILHGCTIGRNALVGMNAVVMDGAVIGEESIVGAMAFVKAGTVIPPRS 121 Query: 96 VVGG 99 ++ G Sbjct: 122 LIAG 125 >gnl|CDD|100044 cd03353, LbH_GlmU_C, N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), C-terminal left-handed beta-helix (LbH) acetyltransferase domain: GlmU is also known as UDP-N-acetylglucosamine pyrophosphorylase. It is a bifunctional bacterial enzyme that catalyzes two consecutive steps in the formation of UDP-N-acetylglucosamine (UDP-GlcNAc), an important precursor in bacterial cell wall formation. The two enzymatic activities, uridyltransferase and acetyltransferase, are carried out by two independent domains. The C-terminal LbH domain possesses the acetyltransferase activity. It catalyzes the CoA-dependent acetylation of GlcN-1-phosphate to GlcNAc-1-phosphate. The LbH domain contains 10 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X. The acetyltransferase active site is located at the interface between two subunits of the active LbH trimer.. Length = 193 Score = 28.9 bits (66), Expect = 0.30 Identities = 14/73 (19%), Positives = 34/73 (46%), Gaps = 11/73 (15%) Query: 3 DNAVVRDCATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRD-----NAKVGGYAKVS- 56 D V++ ++VI+ A + A+V FA ++ + + ++ + + +G +K + Sbjct: 55 DGVVIKA-SSVIEGAVIGNGATVGPFAHLRPGTVLGEGVHIGNFVEIKKSTIGEGSKANH 113 Query: 57 ----GNASVGGNA 65 G+A +G Sbjct: 114 LSYLGDAEIGEGV 126 Score = 26.2 bits (59), Expect = 2.1 Identities = 8/42 (19%), Positives = 20/42 (47%) Query: 67 VRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVVEGDTV 108 + E+G D + ++ G + + V+G + V++ T+ Sbjct: 12 IDGDVEIGVDVVIDPGVILEGKTVIGEDCVIGPNCVIKDSTI 53 >gnl|CDD|100043 cd03352, LbH_LpxD, UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2,3-diacyl-GlcNAc. This constitutes the third step in the lipid A biosynthetic pathway in Gram-negative bacteria. LpxD is a homotrimer, with each subunit consisting of a novel combination of an N-terminal uridine-binding domain, a core lipid-binding left-handed parallel beta helix (LbH) domain, and a C-terminal alpha-helical extension. The LbH domain contains 9 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X).. Length = 205 Score = 27.4 bits (62), Expect = 0.94 Identities = 14/79 (17%), Positives = 27/79 (34%), Gaps = 12/79 (15%) Query: 28 FAQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAF-----VIG- 81 A++ N + N + + +G +G ++ D +G D I Sbjct: 1 SAKIGENVSIGPNAVIGEGVVIGD------GVVIGPGVVIGDGVVIGDDCVIHPNVTIYE 54 Query: 82 FTVISGNARVRGNAVVGGD 100 +I + AV+G D Sbjct: 55 GCIIGDRVIIHSGAVIGSD 73 Score = 24.3 bits (54), Expect = 7.5 Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 6/51 (11%) Query: 53 AKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGDTVV 103 AK+ N S+G NA++ + +G VIG V+ G+ V+G D V+ Sbjct: 2 AKIGENVSIGPNAVIGEGVVIGDGV-VIGPGVVIGD-----GVVIGDDCVI 46 >gnl|CDD|100049 cd03359, LbH_Dynactin_5, Dynactin 5 (or subunit p25); Dynactin is a major component of the activator complex that stimulates dynein-mediated vesicle transport. Dynactin is a heterocomplex of at least eight subunits, including a 150,000-MW protein called Glued, the actin-capping protein Arp1, and dynamatin. In vitro binding experiments show that dynactin enhances dynein-dependent motility, possibly through interaction with microtubules and vesicles. Subunit p25 is part of the pointed-end subcomplex in dynactin that also includes p26, p27, and Arp11. This subcomplex interacts with membranous cargoes. p25 and p27 contain imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X), indicating a left-handed parallel beta helix (LbH) structural domain. Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity.. Length = 161 Score = 26.8 bits (60), Expect = 1.2 Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 1/59 (1%) Query: 3 DNAVVRDCATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASV 61 +N VV A + + N + R +K ++ D T V + + Y+ VSG + Sbjct: 83 ENCVVN-AAQIGSYVHIGKNCVIGRRCIIKDCVKILDGTVVPPDTVIPPYSVVSGRPAR 140 Score = 26.0 bits (58), Expect = 2.6 Identities = 15/68 (22%), Positives = 26/68 (38%), Gaps = 15/68 (22%) Query: 37 VSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIG-FTVISGNARVRGNA 95 + D ++ +N V A++ +G N VIG +I ++ Sbjct: 75 IGDYVFIGENCVVNA-AQIGSYVHIGKNC-------------VIGRRCIIKDCVKILDGT 120 Query: 96 VVGGDTVV 103 VV DTV+ Sbjct: 121 VVPPDTVI 128 >gnl|CDD|100059 cd05635, LbH_unknown, Uncharacterized proteins, Left-handed parallel beta-Helix (LbH) domain: Members in this group are uncharacterized bacterial proteins containing a LbH domain with multiple turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity.. Length = 101 Score = 26.9 bits (60), Expect = 1.3 Identities = 11/41 (26%), Positives = 19/41 (46%) Query: 11 ATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGG 51 A + A + G + ++VK A + NT + K+GG Sbjct: 18 AVIEPFAVIEGPVYIGPGSRVKMGARIYGNTTIGPTCKIGG 58 >gnl|CDD|34718 COG5116, RPN2, 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]. Length = 926 Score = 26.6 bits (58), Expect = 1.6 Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 4/51 (7%) Query: 16 DARVSGNASVSRFAQVKSNAEVSDNTYVRDNA----KVGGYAKVSGNASVG 62 + S A N S++++ R+N K +AK + AS+G Sbjct: 311 ARKFSRFHYAVSLANSFMNLGTSNDSFYRNNLDWLGKASNWAKFTATASLG 361 >gnl|CDD|100042 cd03351, LbH_UDP-GlcNAc_AT, UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic pathway and is also referred to as LpxA. Lipid A is essential for the growth of Escherichia coli and related bacteria. It is also essential for maintaining the integrity of the outer membrane. UDP-GlcNAc acyltransferase is a homotrimer of left-handed parallel beta helix (LbH) subunits. Each subunit contains an N-terminal LbH region with 9 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X), and a C-terminal alpha-helical region.. Length = 254 Score = 26.2 bits (59), Expect = 1.8 Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 2/46 (4%) Query: 65 AIVRDTAEVGGDAFVIG-FTVISGNARVRGNAVVGGDTVVEGDTVL 109 AIV A++G + IG F VI N + V+G V++G T + Sbjct: 6 AIVDPGAKIGENV-EIGPFCVIGPNVEIGDGTVIGSHVVIDGPTTI 50 Score = 25.9 bits (58), Expect = 2.5 Identities = 15/43 (34%), Positives = 23/43 (53%) Query: 58 NASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAVVGGD 100 NA++ G+ + D A +GG + V F I +A V G + V D Sbjct: 132 NATLAGHVEIGDYAIIGGLSAVHQFCRIGRHAMVGGGSGVVQD 174 Score = 25.5 bits (57), Expect = 3.6 Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 11/73 (15%) Query: 37 VSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIG----------FTVIS 86 + +N + +NA + G+ ++ A +GG + V +G A V G + + + Sbjct: 123 IGNNVILANNATLAGHVEIGDYAIIGGLSAVHQFCRIGRHAMVGGGSGVVQDVPPYVIAA 182 Query: 87 GN-ARVRGNAVVG 98 GN AR+RG +VG Sbjct: 183 GNRARLRGLNLVG 195 Score = 24.7 bits (55), Expect = 5.6 Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 6/54 (11%) Query: 53 AKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARV-RGN-----AVVGGD 100 AK+ N +G ++ E+G + VI G + + N A +G Sbjct: 12 AKIGENVEIGPFCVIGPNVEIGDGTVIGSHVVIDGPTTIGKNNRIFPFASIGEA 65 >gnl|CDD|38331 KOG3121, KOG3121, KOG3121, Dynactin, subunit p25 [Cytoskeleton]. Length = 184 Score = 26.1 bits (57), Expect = 2.4 Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 1/58 (1%) Query: 43 VRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGN-AVVGG 99 V + A++G Y + NA +G +++D + D + T++ + + GN A V G Sbjct: 98 VVNAAQIGSYVHLGKNAVIGRRCVLKDCCRILDDTVLPPETLVPPYSTIGGNPAQVVG 155 >gnl|CDD|100051 cd04645, LbH_gamma_CA_like, Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism, involving the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Gamma CAs are trimeric enzymes with left-handed parallel beta helix (LbH) structural domain.. Length = 153 Score = 25.8 bits (58), Expect = 2.7 Identities = 11/54 (20%), Positives = 26/54 (48%), Gaps = 3/54 (5%) Query: 58 NASVGGNAIVRDTAEVGGDAFV-IGFTVISGNARVRGNAVVGGDTVVEGDTVLE 110 N +VG A++ +G + + +G ++ G A + ++V ++V V+ Sbjct: 66 NVTVGHGAVLHG-CTIGDNCLIGMGAIILDG-AVIGKGSIVAAGSLVPPGKVIP 117 >gnl|CDD|30459 COG0110, WbbJ, Acetyltransferase (isoleucine patch superfamily) [General function prediction only]. Length = 190 Score = 25.2 bits (54), Expect = 4.2 Identities = 17/90 (18%), Positives = 32/90 (35%), Gaps = 3/90 (3%) Query: 11 ATVIDDARVSGNASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKVSGN-ASVGGNAIVRD 69 V + + N V + +N+ D A VG G +G A++ Sbjct: 82 ILVGEGITIGDNVVVGPNVTIYTNSHPGDFVTANIGALVGAGPVTIGEDVWIGAGAVILP 141 Query: 70 TAEVGGDAFVIGFTVISGNARVRGNAVVGG 99 +G A + +V++ + V +V G Sbjct: 142 GVTIGEGAVIGAGSVVTKD--VPPYGIVAG 169 >gnl|CDD|113132 pfam04349, MdoG, Periplasmic glucan biosynthesis protein, MdoG. This family represents MdoG, a protein that is necessary for the synthesis of periplasmic glucans. The function of MdoG remains unknown. It has been suggested that it may catalyse the addition of branches to a linear glucan backbone. Length = 484 Score = 24.4 bits (53), Expect = 6.3 Identities = 10/30 (33%), Positives = 15/30 (50%) Query: 23 ASVSRFAQVKSNAEVSDNTYVRDNAKVGGY 52 V+ + SNA V +N +R N + GY Sbjct: 416 HPVTVEPSLHSNAGVVENVSLRYNPVIKGY 445 >gnl|CDD|100050 cd03360, LbH_AT_putative, Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity. A few members are identified as NeuD, a sialic acid (Sia) O-acetyltransferase that is required for Sia synthesis and surface polysaccharide sialylation.. Length = 197 Score = 24.4 bits (54), Expect = 6.6 Identities = 14/76 (18%), Positives = 32/76 (42%) Query: 22 NASVSRFAQVKSNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIG 81 A ++ A++ N ++ + + +G + ++ + G + + A +G A +I Sbjct: 108 GAVINPDARIGDNVIINTGAVIGHDCVIGDFVHIAPGVVLSGGVTIGEGAFIGAGATIIQ 167 Query: 82 FTVISGNARVRGNAVV 97 I A + AVV Sbjct: 168 GVTIGAGAIIGAGAVV 183 >gnl|CDD|36924 KOG1712, KOG1712, KOG1712, Adenine phosphoribosyl transferases [Nucleotide transport and metabolism]. Length = 183 Score = 24.4 bits (53), Expect = 6.8 Identities = 10/40 (25%), Positives = 17/40 (42%) Query: 57 GNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVRGNAV 96 G + + R AEV A VI + G +++G + Sbjct: 136 GTLAAATELLERVGAEVVECACVIELPELKGREKLKGKPL 175 >gnl|CDD|100045 cd03354, LbH_SAT, Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of L-cysteine. This reaction represents a key metabolic point of regulation for the cysteine biosynthetic pathway due to its feedback inhibition by cysteine. The enzyme is a 175 kDa homohexamer, composed of a dimer of homotrimers. Each subunit contains an N-terminal alpha helical region and a C-terminal left-handed beta-helix (LbH) subdomain with 5 turns, each containing a hexapeptide repeat motif characteristic of the acyltransferase superfamily of enzymes. The trimer interface mainly involves the C-terminal LbH subdomain while the dimer (of trimers) interface is mediated by the N-terminal alpha helical subdomain.. Length = 101 Score = 24.3 bits (54), Expect = 8.5 Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 4/65 (6%) Query: 33 SNAEVSDNTYVRDNAKVGGYAKVSGNASVGGNAIVRDTAEVGGDAFVIGFTVISGNARVR 92 A + DN + +GG K G + + D +G A ++G I N ++ Sbjct: 27 ETAVIGDNCTIYQGVTLGGKGKGGG----KRHPTIGDNVVIGAGAKILGNITIGDNVKIG 82 Query: 93 GNAVV 97 NAVV Sbjct: 83 ANAVV 87 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 0.313 0.131 0.358 Gapped Lambda K H 0.267 0.0875 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,096,519 Number of extensions: 48460 Number of successful extensions: 225 Number of sequences better than 10.0: 1 Number of HSP's gapped: 183 Number of HSP's successfully gapped: 84 Length of query: 110 Length of database: 6,263,737 Length adjustment: 76 Effective length of query: 34 Effective length of database: 4,621,453 Effective search space: 157129402 Effective search space used: 157129402 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (23.2 bits)