RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 024996
(259 letters)
>gnl|CDD|212507 cd11648, RsmI, Ribosomal RNA small subunit methyltransferase I,
also known as rRNA (cytidine-2'-O-)-methyltransferase
RsmI. Proteins in this family catalyze the
2-O-methylation of the ribose of cytidine 1402 (C1402)
in 16S rRNA using S-adenosyl-L-methionine (SAM or
Ado-Met) as the methyl donor. RsmI proteins employ the
30S subunit (not the 16S rRNA) as a substrate,
suggesting that the methylation reaction occurs at a
late step during 30S assembly in the cell.
Length = 218
Score = 294 bits (755), Expect = e-101
Identities = 102/174 (58%), Positives = 129/174 (74%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHKFNESQR 142
LYLVATPIGNLEDITLRAL VLK ++I EDTRH+ KLL +Y IK PL+SYH+ NE +R
Sbjct: 1 LYLVATPIGNLEDITLRALEVLKEVDLIACEDTRHTKKLLNHYGIKKPLISYHEHNEEER 60
Query: 143 EQTVLNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAFVAALSASG 202
+ ++ RLK+G+ VAL+SDAGTP ISDPG L + ++ IPVVPIPG SA + ALSASG
Sbjct: 61 AEEIIERLKEGKSVALVSDAGTPLISDPGYRLVRAAIEAGIPVVPIPGPSALITALSASG 120
Query: 203 LATDEFTFVGFLPKHARSRTERLMLSANEVKTQIFYVPPHKLLQFLEETSLLFG 256
L TD FTF+GFLP+ R + L ANE +T +FY PH+LL+ LE+ + + G
Sbjct: 121 LPTDRFTFLGFLPRKKGERRKLLEELANEPRTLVFYESPHRLLKTLEDLAEVGG 174
>gnl|CDD|223390 COG0313, COG0313, Predicted methyltransferases [General function
prediction only].
Length = 275
Score = 256 bits (657), Expect = 6e-86
Identities = 96/180 (53%), Positives = 123/180 (68%)
Query: 77 GPLEPGLYLVATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHK 136
+ LYLV TPIGNL DITLRAL VLK +VI +EDTR + KLL + IKTPL+SYH+
Sbjct: 1 EMMMGTLYLVPTPIGNLADITLRALEVLKEVDVIAAEDTRVTRKLLSHLGIKTPLISYHE 60
Query: 137 FNESQREQTVLNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAFVA 196
NE ++ ++ LK+G+ VAL+SDAGTP ISDPG EL + + I VVP+PG SA +
Sbjct: 61 HNEKEKLPKLIPLLKKGKSVALVSDAGTPLISDPGYELVRAAREAGIRVVPLPGPSALIT 120
Query: 197 ALSASGLATDEFTFVGFLPKHARSRTERLMLSANEVKTQIFYVPPHKLLQFLEETSLLFG 256
ALSASGL + F F GFLP+ ++ R +RL ANE +T IFY PH+LL LE+ + G
Sbjct: 121 ALSASGLPSQRFLFEGFLPRKSKERRKRLEALANEPRTLIFYESPHRLLATLEDIVEVLG 180
>gnl|CDD|184956 PRK14994, PRK14994, SAM-dependent 16S ribosomal RNA C1402 ribose
2'-O-methyltransferase; Provisional.
Length = 287
Score = 186 bits (475), Expect = 2e-58
Identities = 83/174 (47%), Positives = 117/174 (67%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHKFNESQR 142
LY+V TPIGNL DIT RAL VL++ ++I +EDTRH+G LLQ++ I L + H NE Q+
Sbjct: 14 LYIVPTPIGNLADITQRALEVLQAVDLIAAEDTRHTGLLLQHFAINARLFALHDHNEQQK 73
Query: 143 EQTVLNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAFVAALSASG 202
+T+L +L++G+ +AL+SDAGTP I+DPG L + C + I VVP+PG A + ALSA+G
Sbjct: 74 AETLLAKLQEGQNIALVSDAGTPLINDPGYHLVRTCREAGIRVVPLPGPCAAITALSAAG 133
Query: 203 LATDEFTFVGFLPKHARSRTERLMLSANEVKTQIFYVPPHKLLQFLEETSLLFG 256
L +D F + GFLP ++ R + L E +T IFY H+LL LE+ + G
Sbjct: 134 LPSDRFCYEGFLPAKSKGRRDALKALEAEPRTLIFYESTHRLLDSLEDIVAVLG 187
>gnl|CDD|129204 TIGR00096, TIGR00096, probable S-adenosylmethionine-dependent
methyltransferase, YraL family. No member of this
family is characterized, but pfam00590 (tetrapyrrole
methylase) demonstrates homology between this family and
its other members, which include several methylases for
the tetrapyrrole class of compound, as well as the
enzyme diphthine synthase [Unknown function, Enzymes of
unknown specificity].
Length = 276
Score = 144 bits (365), Expect = 5e-42
Identities = 75/167 (44%), Positives = 93/167 (55%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHKFNESQR 142
LY+V TPIGNLEDIT RAL +L ++ EDTR S LL I TP + ++
Sbjct: 2 LYVVTTPIGNLEDITRRALELLACVDLFAEEDTRTSKLLLHLGIIATPKAFHIDNEFQEK 61
Query: 143 EQTVLNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAFVAALSASG 202
+ + +L+ G +A+ SDAG P ISDPG L I VVP+PGA+A AAL ASG
Sbjct: 62 QNLLAAKLEIGNNIAVSSDAGPPLISDPGHLLVACREKANIIVVPLPGAAALTAALCASG 121
Query: 203 LATDEFTFVGFLPKHARSRTERLMLSANEVKTQIFYVPPHKLLQFLE 249
ATD F F GFLPK ++ R A E T FY H+LL L
Sbjct: 122 PATDRFFFGGFLPKKSKRRQALKAYIAEERTTVFFYESHHRLLTTLT 168
>gnl|CDD|212508 cd11649, RsmI_like, Uncharacterized subfamily of the tetrapyrrole
methylase family similar to ribosomal RNA small subunit
methyltransferase I (RsmI). Tetrapyrrole methylase uses
S-AdoMet (S-adenosyl-L-methionine or SAM) in the
methylation of diverse substrates. This uncharacterized
subfamily exhibits sequence similarity to the ribosomal
RNA small subunit methyltransferase I (RsmI), which
catalyzes the 2-O-methylation of the ribose of cytidine
1402 (C1402) in 16S rRNA.
Length = 229
Score = 129 bits (327), Expect = 8e-37
Identities = 61/192 (31%), Positives = 98/192 (51%), Gaps = 19/192 (9%)
Query: 83 LYLVATPIGN---LEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPL--LSYHKF 137
LYL+ P+G + + +++S + + E+ + + + L+ + + P+ L++H
Sbjct: 1 LYLIPNPLGEETPEDVLPAYVKEIVRSLDHFIVENEKTARRFLKKLDPEKPIQELTFHLL 60
Query: 138 NESQREQTV---LNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAF 194
NE E+ + L LK G+ + LIS+AG PG++DPG EL L I VVP+ G S+
Sbjct: 61 NEHTPEEDLPELLAPLKAGKDIGLISEAGCPGVADPGAELVALAHQLGIRVVPLVGPSSI 120
Query: 195 VAALSASGLATDEFTFVGFLPKHARSRTERL----MLSANEVKTQIFYVPPHK------- 243
+ AL ASGL F F G+LP + R + L S E +TQIF P++
Sbjct: 121 LLALMASGLNGQSFAFHGYLPIDKKERKKALKELEQESRKEGQTQIFIETPYRNNKLLED 180
Query: 244 LLQFLEETSLLF 255
LL+ L + L
Sbjct: 181 LLKTLAPNTRLC 192
>gnl|CDD|212499 cd09815, TP_methylase, S-AdoMet dependent tetrapyrrole methylases.
This family uses S-AdoMet (S-adenosyl-L-methionine or
SAM) in the methylation of diverse substrates. Most
members catalyze various methylation steps in cobalamin
(vitamin B12) biosynthesis. There are two distinct
cobalamin biosynthetic pathways in bacteria. The aerobic
pathway requires oxygen, and cobalt is inserted late in
the pathway; the anaerobic pathway does not require
oxygen, and cobalt insertion is the first committed step
towards cobalamin synthesis. The enzymes involved in the
aerobic pathway are prefixed Cob and those of the
anaerobic pathway Cbi. Most of the enzymes are shared by
both pathways and a few enzymes are pathway-specific.
Diphthine synthase and Ribosomal RNA small subunit
methyltransferase I (RsmI) are two superfamily members
that are not involved in cobalamin biosynthesis.
Diphthine synthase participates in the posttranslational
modification of a specific histidine residue in
elongation factor 2 (EF-2) of eukaryotes and archaea to
diphthamide. RsmI catalyzes the 2-O-methylation of the
ribose of cytidine 1402 (C1402) in 16S rRNA using
S-adenosylmethionine (Ado-Met) as the methyl donor.
Length = 224
Score = 97.1 bits (242), Expect = 2e-24
Identities = 42/173 (24%), Positives = 70/173 (40%), Gaps = 12/173 (6%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDTRH---SGKLLQYYNIKTPLLSYHKFNE 139
LY V G+ + +TLRA+ VL+SA+V++ +D K + ++ E
Sbjct: 1 LYFVGAGPGDPDLLTLRAVEVLRSADVVVVDDKVSELLRLKPRAHLPDGAEIVELVDEEE 60
Query: 140 SQ------REQTVLNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASA 193
+T+L +QG V + AG P ++ PG EL + D + V +PG S+
Sbjct: 61 DDHGVLAEVARTLLEAARQGRDVVRLV-AGDPLLAGPGAELRAVAEDAGVDVEVVPGVSS 119
Query: 194 FVAALSASGLATDEFTFVGFLPKHARSRTERLMLSANEVKTQIFYVPPHKLLQ 246
A + +G+ + V F A +T + Y P L
Sbjct: 120 ATAVPAYAGIPLGQ--SVTFADVRDDEPGAEAAALAAAPQTLVLYADPASALA 170
>gnl|CDD|216012 pfam00590, TP_methylase, Tetrapyrrole (Corrin/Porphyrin)
Methylases. This family uses S-AdoMet in the
methylation of diverse substrates. This family includes
a related group of bacterial proteins of unknown
function. This family includes the methylase Dipthine
synthase.
Length = 202
Score = 96.3 bits (240), Expect = 2e-24
Identities = 46/173 (26%), Positives = 73/173 (42%), Gaps = 7/173 (4%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYH--KFNES 140
LY+V G+ E +TLRALR LK A+V++ +D R LL L + E
Sbjct: 2 LYIVGIGPGDPELLTLRALRALKEADVVIGDD-RALEILLDLLRPMGKELELLEGAYEEI 60
Query: 141 QREQTVLNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAFVAALSA 200
L+ G+ V ++ +G P + G+ L + I V IPG S+ AA +
Sbjct: 61 AELLEAAALLRAGKDVVVLV-SGDPLVYGTGSYLVEALEAAGIEVEVIPGISSLQAAAAR 119
Query: 201 SGLATDEFTFVGFLPKHARSRTERLMLSANEVKTQIFYVPPHKL---LQFLEE 250
G+ + V + + RL+ + T + PH+L + L E
Sbjct: 120 LGIPLTDGGVVSLHGRGLETLRARLLEALLAGDTLVLLTDPHRLAEIAELLLE 172
>gnl|CDD|212510 cd11724, TP_methylase_like, Uncharacterized subfamily of S-AdoMet
dependent tetrapyrrole methylases. TP-methylases use
S-AdoMet (S-adenosyl-L-methionine or SAM) in the
methylation of diverse substrates. Most members catalyze
various methylation steps in cobalamin (vitamin B12)
biosynthesis, other members like Diphthine synthase and
Ribosomal RNA small subunit methyltransferase I (RsmI)
act on other substrates. The function of this subfamily
is not known.
Length = 255
Score = 58.1 bits (141), Expect = 5e-10
Identities = 42/148 (28%), Positives = 56/148 (37%), Gaps = 36/148 (24%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDT-----------------------RHSG 119
LYLV G+ ++ITLRAL V+ A++I + G
Sbjct: 3 LYLVGVGPGDPDNITLRALEVIAKADIIFCPKEIVKRFADYLKGKPVLEDPWKLFWHYGG 62
Query: 120 KLLQYYNIKTPLLSYHKFNES----QREQ---TVLNRLKQGEIVALISDAGTPGISDPGT 172
K S + E QRE+ + L QG+ VAL+ D G P I P
Sbjct: 63 KPW---ENLEAEKSPREAFEEEKKRQREEFVKVIREALAQGKNVALL-DGGDPTIYGPSH 118
Query: 173 ELAKLCVDEKIPVVPIPGASAFVAALSA 200
L + D IPG S F AA +A
Sbjct: 119 WLMEGFDDL--DPEIIPGVSCFNAANAA 144
>gnl|CDD|223086 COG0007, CysG, Uroporphyrinogen-III methylase [Coenzyme
metabolism].
Length = 244
Score = 55.3 bits (134), Expect = 3e-09
Identities = 39/147 (26%), Positives = 63/147 (42%), Gaps = 28/147 (19%)
Query: 84 YLV-ATPIGNLEDITLRALRVLKSANVIL-----SEDTRHSGKLLQYYNIKTPLLSYHKF 137
YLV A P G+ +TLRALR L+ A+V+L E+ +L + K
Sbjct: 7 YLVGAGP-GDPGLLTLRALRALQEADVVLYDRLVPEE------VLALARRDAERIYVGKR 59
Query: 138 ----NESQRE--QTVLNRLKQGEIVA-LISDAGTPGISDPGTELAKLCVDEKIPVVPIPG 190
++ Q E ++ ++G+ V L G P I G E + + I +PG
Sbjct: 60 PGGHSKPQDEINALLVELAREGKRVVRLKG--GDPYIFGRGGEEIEALAEAGIEFEVVPG 117
Query: 191 ASAFVAALSASGLA------TDEFTFV 211
++ +AA + +G+ FTFV
Sbjct: 118 ITSAIAAPAYAGIPLTHRGVASSFTFV 144
>gnl|CDD|212506 cd11647, Diphthine_synthase, Diphthine synthase, also known as
DPH5. Diphthine synthase, also known as diphthamide
biosynthesis S-adenosylmethionine-dependent
methyltransferase, participates in the posttranslational
modification of a specific histidine residue in
elongation factor 2 (EF-2) of eukaryotes and archaea to
diphthamide. It catalyzes the trimethylation step in
diphthamide biosynthesis. Diphthamide is the target of
diphtheria toxin, which ADP-ribosylates diphthamide and
inhibits protein synthesis, leading to host cell death.
Length = 241
Score = 53.7 bits (130), Expect = 1e-08
Identities = 34/128 (26%), Positives = 54/128 (42%), Gaps = 12/128 (9%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSE-------DTRHSGKLLQYYNIKTPLLSYH 135
LYLV +G+ +DITL+ L +K A+ + E L ++Y + +
Sbjct: 2 LYLVGLGLGDEKDITLKGLEAVKKADKVYLEAYTSILMGGTLE-ALEEFYGKEIIVADRE 60
Query: 136 KFNESQREQTVLNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAFV 195
E E +L K+ ++ L+ G P I+ ++L + I V I AS
Sbjct: 61 DVEEESDE--ILEEAKEKDVALLV--VGDPFIATTHSDLRLRAKERGIEVRVIHNASILN 116
Query: 196 AALSASGL 203
A S SGL
Sbjct: 117 AVGSCSGL 124
>gnl|CDD|223942 COG1010, CobJ, Precorrin-3B methylase [Coenzyme metabolism].
Length = 249
Score = 52.2 bits (126), Expect = 4e-08
Identities = 34/125 (27%), Positives = 57/125 (45%), Gaps = 17/125 (13%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDT------RHSGKLLQYYNIKTPLLSYHK 136
LY+V G+ E +T A R L+ A+VI+ T GK + I++ +
Sbjct: 5 LYVVGIGPGDPELMTPEARRALEEADVIVGYTTYLDLIELRPGKEV----IRSGMR---- 56
Query: 137 FNESQREQTVLNRLKQGEIVALIS--DAGTPGISDPGTELAKLCVDEKIPVVPIPGASAF 194
E +R + + +G VAL+S D G G++ E A+ + V +PG +A
Sbjct: 57 -EEIERAKEAIELAAEGRDVALVSSGDPGVYGMAGLVLEAAEEEGWYDVDVEVVPGVTAA 115
Query: 195 VAALS 199
+AA +
Sbjct: 116 LAAAA 120
>gnl|CDD|212505 cd11646, Precorrin_3B_C17_MT, Precorrin-3B C(17)-methyltransferase
(CobJ/CbiH). Precorrin-3B C(17)-methyltransferase
participates in the pathway toward the biosynthesis of
cobalamin (vitamin B12). There are two distinct
cobalamin biosynthetic pathways. The aerobic pathway
requires oxygen, and cobalt is inserted late in the
pathway; the anaerobic pathway does not require oxygen,
and cobalt insertion is the first committed step towards
cobalamin synthesis. This model includes CobJ of the
aerobic pathway and CbiH of the anaerobic pathway, both
as stand-alone enzymes and when CobJ forms part of a
bifunctional enzyme. In the aerobic pathway, once CobG
has generated precorrin-3b, CobJ catalyzes the
methylation of precorrin-3b at C-17 to form precorrin-4
(the extruded methylated C-20 fragment is left attached
as an acyl group at C-1). In the corresponding anaerobic
pathway, CbiH carries out this ring contraction, using
cobalt-precorrin-3b as a substrate to generate a
tetramethylated delta-lactone.
Length = 240
Score = 50.5 bits (122), Expect = 2e-07
Identities = 34/123 (27%), Positives = 60/123 (48%), Gaps = 17/123 (13%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHKF----- 137
LY+V G+ + +T RA ++ A+V++ T Y ++ LL +
Sbjct: 3 LYVVGIGPGDPDLMTPRAREAIEEADVVVGYKT--------YLDLIEDLLEGKEVISSGM 54
Query: 138 -NESQREQTVLNRLKQGEIVALIS--DAGTPGISDPGTELAKLCVDEKIPVVPIPGASAF 194
E +R + + ++G+ VAL+S D G G++ ELA+ D+ + V IPG +A
Sbjct: 55 GEEVERARLAVELAREGKTVALVSSGDPGVYGMAGLVLELAEKEGDD-VEVEVIPGVTAA 113
Query: 195 VAA 197
+AA
Sbjct: 114 LAA 116
>gnl|CDD|224711 COG1798, DPH5, Diphthamide biosynthesis methyltransferase
[Translation, ribosomal structure and biogenesis].
Length = 260
Score = 47.7 bits (114), Expect = 1e-06
Identities = 38/127 (29%), Positives = 59/127 (46%), Gaps = 10/127 (7%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSED--TRHSG----KLLQYYNIKTPLLSYHK 136
LYLV + + DITL+ L ++ A+ + +E + G KL + + LL
Sbjct: 2 LYLVGLGLYDEGDITLKGLEAVRKADRVYAEFYTSILLGSNLEKLEELIGKEVILLDRED 61
Query: 137 FNESQREQTVLNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAFVA 196
E+ R +L+R K + VAL+ AG P ++ +L I V I GAS A
Sbjct: 62 LEENSRS--ILDRAKDKD-VALLV-AGDPMVATTHVDLRIEAKRRGIEVRVIHGASIINA 117
Query: 197 ALSASGL 203
A+ +GL
Sbjct: 118 AIGLTGL 124
>gnl|CDD|233424 TIGR01466, cobJ_cbiH, precorrin-3B C17-methyltransferase. This
model represents precorrin-3B C17-methyltransferase, one
of two methyltransferases commonly referred to as
precorrin-3 methylase (the other is precorrin-4
C11-methyltransferase, EC 2.1.1.133). This enzyme
participates in the pathway toward the biosynthesis of
cobalamin and related products. Members of this family
may appear as fusion proteins with other enzymes of
cobalamin biosynthesis [Biosynthesis of cofactors,
prosthetic groups, and carriers, Heme, porphyrin, and
cobalamin].
Length = 239
Score = 46.9 bits (112), Expect = 2e-06
Identities = 34/126 (26%), Positives = 51/126 (40%), Gaps = 19/126 (15%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHKF----- 137
LY+V G E +T A L A+VI+ T Y ++ L+ +
Sbjct: 1 LYVVGIGPGAEELMTPEAKEALAEADVIVGYKT--------YLDLIEDLIPGKEVVTSGM 52
Query: 138 -NESQREQTVLNRLKQGEIVALIS--DAGTPGISDPGTELAKLC-VDEKIPVVPIPGASA 193
E R + + +G VAL+S D G G++ E + + I V IPG +A
Sbjct: 53 REEIARAELAIELAAEGRTVALVSSGDPGIYGMAALVFEALEKKGAEVDIEV--IPGITA 110
Query: 194 FVAALS 199
AA S
Sbjct: 111 ASAAAS 116
>gnl|CDD|233426 TIGR01469, cobA_cysG_Cterm, uroporphyrin-III C-methyltransferase.
This model represents enzymes, or enzyme domains, with
uroporphyrin-III C-methyltransferase activity. This
enzyme catalyzes the first step committed to the
biosynthesis of either siroheme or cobalamin (vitamin
B12) rather than protoheme (heme). Cobalamin contains
cobalt while siroheme contains iron. Siroheme is a
cofactor for nitrite and sulfite reductases and
therefore plays a role in cysteine biosynthesis; many
members of this family are CysG, siroheme synthase, with
an additional N-terminal domain and with additional
oxidation and iron insertion activities [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 236
Score = 46.4 bits (111), Expect = 4e-06
Identities = 41/132 (31%), Positives = 67/132 (50%), Gaps = 20/132 (15%)
Query: 84 YLV-ATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLL------SYHK 136
YLV A P G+ E +TL+ALR+L+ A+V+L D S ++L Y + L+ H
Sbjct: 3 YLVGAGP-GDPELLTLKALRLLQEADVVLY-DALVSPEILAYAPPQAELIDVGKRPGCHS 60
Query: 137 FNESQREQTVLNRL-----KQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGA 191
Q E +NRL ++G+ V + G P + G E A+ + IP +PG
Sbjct: 61 K--KQEE---INRLLVELAREGKKVVRLK-GGDPFVFGRGGEEAEALAEAGIPFEVVPGV 114
Query: 192 SAFVAALSASGL 203
++ +AA + +G+
Sbjct: 115 TSAIAAAAYAGI 126
>gnl|CDD|212504 cd11645, Precorrin_2_C20_MT, Precorrin-2 C20-methyltransferase,
also named CobI or CbiL. Precorrin-2
C20-methyltransferase participates in the pathway toward
the biosynthesis of cobalamin (vitamin B12). There are
two distinct cobalamin biosynthetic pathways in
bacteria. The aerobic pathway requires oxygen, and
cobalt is inserted late in the pathway; the anaerobic
pathway does not require oxygen, and cobalt insertion is
the first committed step towards cobalamin synthesis.
Precorrin-2 C20-methyltransferase catalyzes methylation
at the C-20 position of a cyclic tetrapyrrole ring of
precorrin-2 using S-adenosylmethionine as a methyl group
source to produce precorrin-3A. In the anaerobic
pathway, cobalt is inserted into precorrin-2 by CbiK to
generate cobalt-precorrin-2, which is the substrate for
CbiL, a C20 methyltransferase. In Clostridium difficile,
CbiK and CbiL are fused into a bifunctional enzyme. In
the aerobic pathway, the precorrin-2
C20-methyltransferase is named CobI. This family
includes CbiL and CobI precorrin-2
C20-methyltransferases, both as stand-alone enzymes and
when CbiL forms part of a bifunctional enzyme.
Length = 226
Score = 44.8 bits (107), Expect = 1e-05
Identities = 46/205 (22%), Positives = 78/205 (38%), Gaps = 49/205 (23%)
Query: 77 GPLEPGLYLVATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHK 136
GP +P L +TL+A+R+L+ A+VI ++ + L+ +
Sbjct: 8 GPGDPEL------------LTLKAVRILREADVIAVPGSKAGEGSAALIIVVAYLIPEKE 55
Query: 137 F--------------NESQRE--QTVLNRLKQGEIVALISDAGTPGISDPGT-----ELA 175
E+ E + L+ G+ VA ++ + DP L
Sbjct: 56 ILPLEFPMTKDKEVLEEAWDEAAAEIAAELEAGKDVAFLT------LGDPSLYSTFSYLL 109
Query: 176 KLCVDEKIPVVPIPGASAFVAALSASG--LAT-DEFTFVGFLPKHARSRTERLMLSANEV 232
+ + + V IPG ++F AA + G LA DE + LP A E L +
Sbjct: 110 RRLREPGVEVETIPGITSFSAAAARLGIPLAEGDERLAI--LP--ATLGEEELEEALELF 165
Query: 233 KTQIFY-VPPH--KLLQFLEETSLL 254
T + V + ++ + LEE LL
Sbjct: 166 DTVVLMKVGRNLDEVRELLEEAGLL 190
>gnl|CDD|235231 PRK04160, PRK04160, diphthine synthase; Provisional.
Length = 258
Score = 44.5 bits (106), Expect = 2e-05
Identities = 33/127 (25%), Positives = 58/127 (45%), Gaps = 9/127 (7%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSED--TRHSG----KLLQYYNIKTPLLSYHK 136
LY + + + DITL+ L L++A+ + +E + G KL + + +L +
Sbjct: 2 LYFIGLGLYDERDITLKGLEALRNADKVYAEFYTSILMGTTIEKLEELIGKEIIVLD-RE 60
Query: 137 FNESQREQTVLNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAFVA 196
E + E+ +L K+ + L AG P ++ +L I V I G S + A
Sbjct: 61 DVEQESEKIILEEAKEKNVAFLT--AGDPMVATTHVDLRLEAKKRGIEVRVIHGVSIYSA 118
Query: 197 ALSASGL 203
A+S +GL
Sbjct: 119 AISLTGL 125
>gnl|CDD|225152 COG2243, CobF, Precorrin-2 methylase [Coenzyme metabolism].
Length = 234
Score = 43.0 bits (102), Expect = 5e-05
Identities = 34/143 (23%), Positives = 55/143 (38%), Gaps = 27/143 (18%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDTRHSGKL-----LQYYNIKTPLLSYH-- 135
LY V G+ E +TL+A+R LK A+V+ + G L Y + ++ H
Sbjct: 4 LYGVGLGPGDPELLTLKAIRALKKADVVYVPSKKGKGSLAREIVEDYLTPGSRIVELHFP 63
Query: 136 --KFNESQREQ-------TVLNRLKQGEIVALISDAGTPGISDP---GT--ELAKLCVDE 181
+ E V L+ G VA ++ + DP T L + +
Sbjct: 64 MTTDMREELEDAWEEAAAEVAAELEAGRDVAFLT------LGDPTFYSTFMYLLERLRER 117
Query: 182 KIPVVPIPGASAFVAALSASGLA 204
V +PG S+F A + G+
Sbjct: 118 GFEVEVVPGVSSFSACAARLGVP 140
>gnl|CDD|225150 COG2241, CobL, Precorrin-6B methylase 1 [Coenzyme metabolism].
Length = 210
Score = 42.2 bits (100), Expect = 9e-05
Identities = 36/153 (23%), Positives = 59/153 (38%), Gaps = 12/153 (7%)
Query: 91 GNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHKFNESQREQTVLNRL 150
G E +TL A+ ++ A+V+ RH L + + Y ES E +L
Sbjct: 10 GGPEGLTLAAIEAIRRADVVAGSK-RHLELLPPLIKAERIIWPYPFDAESLEE--ILAER 66
Query: 151 KQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAFVAALSASGLATDEFTF 210
K ++V L S G P S G L + E++ + IPG S+ A + G +
Sbjct: 67 KGRDVVVLAS--GDPLFSGVGRLLRRKFSCEEVEI--IPGISSVQLAAARLGWPLQDTEV 122
Query: 211 VGFLPKHARSRTERLMLSANEVKTQIFYVPPHK 243
+ H R L+ E ++ + P
Sbjct: 123 ISL---HGRPVE--LLRPLLENGRRLVILTPDD 150
>gnl|CDD|212501 cd11642, SUMT, Uroporphyrin-III C-methyltransferase
(S-Adenosyl-L-methionine:uroporphyrinogen III
methyltransferase, SUMT). SUMT, an enzyme of the
cobalamin and siroheme biosynthetic pathway, catalyzes
the transformation of uroporphyrinogen III into
precorrin-2. It transfers two methyl groups from
S-adenosyl-L-methionine to the C-2 and C-7 atoms of
uroporphyrinogen III to yield precorrin-2 via the
intermediate formation of precorrin-1. SUMT is the first
enzyme committed to the biosynthesis of siroheme or
cobalamin (vitamin B12), and precorrin-2 is a common
intermediate in the biosynthesis of corrinoids such as
vitamin B12, siroheme and coenzyme F430. In some
organisms, the SUMT domain is fused to the precorrin-2
oxidase/ferrochelatase domain to form siroheme synthase
or to uroporphyrinogen-III synthase to form bifunctional
uroporphyrinogen-III methylase/uroporphyrinogen-III
synthase.
Length = 233
Score = 42.0 bits (100), Expect = 1e-04
Identities = 41/164 (25%), Positives = 63/164 (38%), Gaps = 60/164 (36%)
Query: 83 LYLV-ATPIGNLEDITLRALRVLKSANVIL-----SEDTRHSGKLLQYYNIKTPLLS--- 133
+YLV A P G+ E +TL+ALR+L+ A+V+L S + +L L+
Sbjct: 2 VYLVGAGP-GDPELLTLKALRLLQEADVVLYDRLVSPE------ILDLAPPDAELIYVGK 54
Query: 134 ---YHKFNESQRE------------QTVLNRLKQGEIVALISDAGTPGISDP-----GTE 173
H Q E + V+ RLK G DP G E
Sbjct: 55 RPGKHSL--PQEEINELLVEYAREGKRVV-RLKGG---------------DPFVFGRGGE 96
Query: 174 LAKLCVDEKIPVVPIPGASAFVAALSASGL------ATDEFTFV 211
+ + IP +PG ++ +AA + +G+ TFV
Sbjct: 97 EIEALREAGIPFEVVPGITSAIAAPAYAGIPLTHRGVASSVTFV 140
>gnl|CDD|185500 PTZ00175, PTZ00175, diphthine synthase; Provisional.
Length = 270
Score = 41.1 bits (97), Expect = 2e-04
Identities = 31/127 (24%), Positives = 58/127 (45%), Gaps = 11/127 (8%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSED------TRHSGKLLQYYNIKTPLLSYHK 136
LY++ +G+ +DIT++ L +KSA+V+ E + KL ++Y + + +
Sbjct: 3 LYIIGLGLGDEKDITVKGLEAVKSADVVYLESYTSILINSNKEKLEEFYGKPV-IEADRE 61
Query: 137 FNESQREQTVLNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAFVA 196
E + +L K+ + L+ G P + T+L + I V I AS +
Sbjct: 62 MVEEGCD-EILEEAKEKNVAFLV--VGDPFCATTHTDLYLRAKKKGIEVEVIHNAS-IMN 117
Query: 197 ALSASGL 203
A+ +GL
Sbjct: 118 AIGCTGL 124
>gnl|CDD|212503 cd11644, Precorrin-6Y-methylase, Precorrin-6Y methyltransferase,
the cobalamin biosynthesis enzyme CbiE. Precorrin-6Y
methyltransferase participates in the pathway toward the
biosynthesis of cobalamin (vitamin B12). There are two
distinct cobalamin biosynthetic pathways in bacteria.
The aerobic pathway requires oxygen, and cobalt is
inserted late in the pathway; the anaerobic pathway does
not requires oxygen, and cobalt insertion is the first
committed step towards cobalamin synthesis. This model
represents the CbiE subunit of precorrin-6Y
C5,15-methyltransferase from the anaerobic pathway, a
bifunctional enzyme that catalyzes two methylations (at
C-5 and C-15) in precorrin-6Y, as well as the
decarboxylation of the acetate side chain located in
ring C, in order to generate precorrin-8X. In the
anaerobic pathway, two enzymes are required to produce
precorrin-8X: CbiE and CbiT, which can be fused as CbiET
(sometimes called CobL). In the aerobic pathway, the
bifunctional enzyme is called CobL.
Length = 201
Score = 40.2 bits (95), Expect = 3e-04
Identities = 33/141 (23%), Positives = 53/141 (37%), Gaps = 19/141 (13%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVIL-SEDTRHSGKLLQYYNIKTPLLSYHKFNESQ 141
+ +V G + +T A ++ A+V++ + RH +L + L E
Sbjct: 1 ITVVGIGPGGPDGLTPAAREAIEEADVLVGGK--RH-LELFPDLGAEKIPLPSDDLAE-- 55
Query: 142 REQTVLNRLKQ--GEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAFVAALS 199
+L RL +V L S G P G LA+ E++ V IPG S+ A +
Sbjct: 56 ----LLERLAAAGRRVVVLAS--GDPLFYGIGATLARRLGAEEVEV--IPGISSVQLAFA 107
Query: 200 ASGLATDEFTFVGFLPKHARS 220
G + V H R
Sbjct: 108 RLGWPWQDAAVVSL---HGRD 125
>gnl|CDD|200107 TIGR01465, cobM_cbiF, precorrin-4 C11-methyltransferase. This
model represents precorrin-4 C11-methyltransferase, one
of two methyltransferases commonly referred to as
precorrin-3 methylase (the other is precorrin-3B
C17-methyltransferase, EC 2.1.1.131). This enzyme
participates in the pathway toward the biosynthesis of
cobalamin and related products [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 247
Score = 39.6 bits (93), Expect = 8e-04
Identities = 29/120 (24%), Positives = 59/120 (49%), Gaps = 1/120 (0%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHKFNESQR 142
+Y + G+ + IT++ ++++SA+VIL + +LL + +++ + +
Sbjct: 1 VYFIGAGPGDPDLITVKGRKLIESADVILYAGSLVPPELLAHCRPGAEVVNSAGMSLEEI 60
Query: 143 EQTVLNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAFVAALSASG 202
+ + ++G+ VA + +G P I E +L IP +PG S+F AA +A G
Sbjct: 61 VDIMSDAHREGKDVARLH-SGDPSIYGAIAEQMRLLEALGIPYEVVPGVSSFFAAAAALG 119
>gnl|CDD|233425 TIGR01467, cobI_cbiL, precorrin-2 C20-methyltransferase. This
model represents precorrin-2 C20-methyltransferase, one
of several closely related
S-adenosylmethionine-dependent methyltransferases
involved in cobalamin (vitamin B12) biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Heme, porphyrin, and cobalamin].
Length = 230
Score = 38.4 bits (90), Expect = 0.002
Identities = 35/138 (25%), Positives = 59/138 (42%), Gaps = 18/138 (13%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHK------ 136
LY V G+ E IT++AL L+SA+VI ++ + L ++ L
Sbjct: 3 LYGVGVGPGDPELITVKALEALRSADVIAVPASKKGRESLARKIVEDYLKPNDTRILELV 62
Query: 137 FNESQRE-----------QTVLNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPV 185
F ++ + V L++G VA ++ G P + + L + I V
Sbjct: 63 FPMTKDRDELEKAWDEAAEAVAAELEEGRDVAFLTL-GDPSLYSTFSYLLQRLQGMGIEV 121
Query: 186 VPIPGASAFVAALSASGL 203
+PG ++F A SA+GL
Sbjct: 122 EVVPGITSFAACASAAGL 139
>gnl|CDD|225430 COG2875, CobM, Precorrin-4 methylase [Coenzyme metabolism].
Length = 254
Score = 38.0 bits (89), Expect = 0.003
Identities = 32/124 (25%), Positives = 61/124 (49%), Gaps = 14/124 (11%)
Query: 91 GNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHKFNESQREQTVLNRL 150
G+ + IT++ R+L+ A+V++ + +LL+Y +++ + +++ +
Sbjct: 13 GDPDLITVKGQRLLEKADVVIYAGSLVPPELLEYCRPDAEIVNSASLTLEEIIDLMVDAV 72
Query: 151 KQGEIVA-LISDAGTPGI----SDPGTELAKLCVDEKIPVVPIPGASAFVAALSASGLAT 205
++G+ V L S G P I ++ EL L IP +PG S+F AA +A G+
Sbjct: 73 REGKDVVRLHS--GDPSIYGALAEQMRELEAL----GIPYEVVPGVSSFAAAAAALGI-- 124
Query: 206 DEFT 209
E T
Sbjct: 125 -ELT 127
>gnl|CDD|235609 PRK05787, PRK05787, cobalt-precorrin-6Y C(5)-methyltransferase;
Validated.
Length = 210
Score = 36.4 bits (85), Expect = 0.006
Identities = 37/175 (21%), Positives = 58/175 (33%), Gaps = 35/175 (20%)
Query: 91 GNLEDITLRALRVLKSANVI---------LSEDTRHSGKLLQYYNIKTPLLSYHKFNESQ 141
G+ E +TL+AL ++ A+V+ E +L
Sbjct: 10 GDPEYLTLKALEAIRKADVVVGSKRVLELFPELIDGEAFVLT------------AGLRDL 57
Query: 142 REQTVLNRLKQGEIVALISDAGTPGISDPG-TELAKLCVDEKIPVVPIPGASAFVAALSA 200
E + K +V L + G P S G + V E + V IPG S+ A +
Sbjct: 58 LEW-LELAAKGKNVVVLST--GDPLFSGLGKLLKVRRAVAEDVEV--IPGISSVQYAAAR 112
Query: 201 SGLATDEFTFVGFLPKHARS--RTERLMLSANEVKTQIF---YVPPHKLLQFLEE 250
G+ ++ F H R E L N K + P ++ L E
Sbjct: 113 LGIDMNDVVFTTS---HGRGPNFEELEDLLKNGRKVIMLPDPRFGPKEIAAELLE 164
>gnl|CDD|233878 TIGR02467, CbiE, precorrin-6y C5,15-methyltransferase
(decarboxylating), CbiE subunit. This model recognizes
the CbiE methylase which is responsible, in part (along
with CbiT), for methylating precorrin-6y (or
cobalt-precorrin-6y) at both the 5 and 15 positions as
well as the concomitant decarbozylation at C-12. In many
organisms, this protein is fused to the CbiT subunit.
The fused protein, when found in organisms catalyzing
the oxidative version of the cobalamin biosynthesis
pathway, is called CobL.
Length = 204
Score = 36.5 bits (85), Expect = 0.007
Identities = 29/132 (21%), Positives = 53/132 (40%), Gaps = 13/132 (9%)
Query: 91 GNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHKFNESQRE--QTVLN 148
G E +T A+ ++ A++++ RH L + K ++ + E + +
Sbjct: 7 GGPELLTPAAIEAIRKADLVVGG-ERHLELLAELIGEKREII---LTYKDLDELLEFIAA 62
Query: 149 RLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAFVAALSASGLATDEF 208
K+ +V L S G P G LA+ E++ + IPG S+ A + GL +
Sbjct: 63 TRKEKRVVVLAS--GDPLFYGIGRTLAERLGKERLEI--IPGISSVQYAFARLGLPWQDA 118
Query: 209 TFVGFLPKHARS 220
+ H R
Sbjct: 119 VVISL---HGRE 127
>gnl|CDD|178232 PLN02625, PLN02625, uroporphyrin-III C-methyltransferase.
Length = 263
Score = 36.1 bits (84), Expect = 0.010
Identities = 48/179 (26%), Positives = 76/179 (42%), Gaps = 30/179 (16%)
Query: 81 PG-LYLVATPIGNLEDITLRALRVLKSANVIL-----SED----TRHSGKLLQYYNIKTP 130
PG ++LV T G+ + +TL+ALR+L++A+V+L S D +LL Y K
Sbjct: 14 PGNVFLVGTGPGDPDLLTLKALRLLQTADVVLYDRLVSPDILDLVPPGAELL--YVGKRG 71
Query: 131 LLSYHKFNESQREQTVLNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPG 190
YH + + + +L+ + G+ V + G P + G E IPV +PG
Sbjct: 72 --GYHSRTQEEIHELLLSFAEAGKTVVRLK-GGDPLVFGRGGEEMDALRKNGIPVTVVPG 128
Query: 191 -ASAFVAALSAS------GLATDEFTFVGFLPKHARSRTERLM----LSANEVKTQIFY 238
+A A G+AT V FL H R + +A+ T + Y
Sbjct: 129 ITAAIGAPAELGIPLTHRGVATS----VRFLTGHDREGGTDPLDVAEAAADPDTTLVVY 183
>gnl|CDD|233007 TIGR00522, dph5, diphthine synthase. Alternate name: diphthamide
biosynthesis S-adenosylmethionine-dependent
methyltransferase. This protein participates in the
modification of a specific His of elongation factor 2 of
eukarotes and Archaea to diphthamide. The protein was
characterized in Saccharomyces cerevisiae and designated
DPH5 [Protein fate, Protein modification and repair].
Length = 257
Score = 35.6 bits (82), Expect = 0.015
Identities = 31/134 (23%), Positives = 60/134 (44%), Gaps = 14/134 (10%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLL--------QYYNIKTPLLSY 134
LYL+ + + DI+++ L +K A+ + +E ++ KLL +++ + +L
Sbjct: 2 LYLIGLGLYDENDISVKGLEAIKKADEVYAE--FYTSKLLGSSIEEIEEFFGKRVVVLER 59
Query: 135 HKFNESQREQTVLNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAF 194
E+ ++ R K ++ L+ AG P ++ T+L + I I GAS
Sbjct: 60 SDVEENSFR--LIERAKSKDVALLV--AGDPMVATTHTDLKLEAKRKGIETRIIHGASIS 115
Query: 195 VAALSASGLATDEF 208
A +GL +F
Sbjct: 116 SAVCGLTGLQLYKF 129
>gnl|CDD|235512 PRK05576, PRK05576, cobalt-precorrin-2 C(20)-methyltransferase;
Validated.
Length = 229
Score = 34.9 bits (81), Expect = 0.023
Identities = 43/194 (22%), Positives = 80/194 (41%), Gaps = 36/194 (18%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLL------QYYNIKTPLLSYH- 135
LY + G+ E +T++A R+L+ A+V+ + +R G L Y +T ++ H
Sbjct: 4 LYGIGLGPGDPELLTVKAARILEEADVVYAPASRKGGGSLALNIVRPYLKEETEIVELHF 63
Query: 136 --KFNESQRE-------QTVLNRLKQGEIVALISDAGTPGISDP---GT--ELAKLCVDE 181
+E ++E + + ++G+ VA I+ + DP T L +
Sbjct: 64 PMSKDEEEKEAVWKENAEEIAAEAEEGKNVAFIT------LGDPNLYSTFSHLLEYLKCH 117
Query: 182 KIPVVPIPGASAFVAALSASG--LATDEFTFVGFLPKHARSRTERLMLSANEVKTQIF-- 237
I V +PG S+F A S +G LA + L +R + + + + +
Sbjct: 118 DIEVETVPGISSFTAIASRAGVPLAMGD----ESLAIIPATREALIEQALTDFDSVVLMK 173
Query: 238 -YVPPHKLLQFLEE 250
Y + + LEE
Sbjct: 174 VYKNFALIEELLEE 187
>gnl|CDD|235597 PRK05765, PRK05765, precorrin-3B C17-methyltransferase;
Provisional.
Length = 246
Score = 34.4 bits (79), Expect = 0.035
Identities = 37/130 (28%), Positives = 61/130 (46%), Gaps = 21/130 (16%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLL------SYHK 136
LY+V G+ E T++A ++ +NVI+ +T Y + + LL
Sbjct: 4 LYIVGIGPGSKEQRTIKAQEAIEKSNVIIGYNT--------YLRLISDLLDGKEVIGARM 55
Query: 137 FNESQREQTVLNRLKQGEIVALISDAGTP---GISDPGTEL-AKLCVDEKIPVVPIPGAS 192
E R T + + +G IVAL+S G P G++ EL ++ +D + V IPG +
Sbjct: 56 KEEIFRANTAIEKALEGNIVALVSS-GDPQVYGMAGLVFELISRRKLDVDVEV--IPGVT 112
Query: 193 AFVAALSASG 202
A +AA + G
Sbjct: 113 AALAAAARLG 122
>gnl|CDD|235711 PRK06136, PRK06136, uroporphyrin-III C-methyltransferase; Reviewed.
Length = 249
Score = 34.4 bits (80), Expect = 0.041
Identities = 42/139 (30%), Positives = 61/139 (43%), Gaps = 34/139 (24%)
Query: 84 YLV-ATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHKFNESQR 142
YLV A P G+ + ITL+ +R+L+ A+V+L +D S ++L Y L+ K
Sbjct: 6 YLVGAGP-GDPDLITLKGVRLLEQADVVLYDDLV-SPEILAYAKPDAELIYVGK------ 57
Query: 143 EQTVLNR-----LKQGEIVALISDAGTPGIS-------DP------GTELAKLCVDEKIP 184
R KQ EI L+ D G DP G EL L IP
Sbjct: 58 ------RAGRHSTKQEEINRLLVDYARKGKVVVRLKGGDPFVFGRGGEELEAL-EAAGIP 110
Query: 185 VVPIPGASAFVAALSASGL 203
+PG +A +AA + +G+
Sbjct: 111 YEVVPGITAAIAAAAYAGI 129
>gnl|CDD|178725 PLN03183, PLN03183, acetylglucosaminyltransferase family protein;
Provisional.
Length = 421
Score = 34.4 bits (79), Expect = 0.049
Identities = 32/100 (32%), Positives = 47/100 (47%), Gaps = 17/100 (17%)
Query: 8 PLMANSLATTGLSKTSWQSRPLLSFLRTQTLLNSLSLYPKINYLLLCSCSQSQTSPDFSN 67
PL+ SL L TS+ + L+S LRT + S+ + N QT +F+
Sbjct: 13 PLVITSLVCVFLLATSF-NMGLVSSLRTINSIFSIFPLSRTN----------QTRLEFAE 61
Query: 68 LILEQSSKRGPLEPGL----YLVATPIGNLEDI--TLRAL 101
+ QS P++ L YLV+ G+LE + TLRAL
Sbjct: 62 SKVNQSPHPPPVQDKLPRFAYLVSGSKGDLEKLWRTLRAL 101
>gnl|CDD|212500 cd11641, Precorrin-4_C11-MT, Precorrin-4 C11-methyltransferase
(CbiF/CobM). Precorrin-4 C11-methyltransferase
participates in the pathway toward the biosynthesis of
cobalamin (vitamin B12). There are two distinct
cobalamin biosynthetic pathways in bacteria. The aerobic
pathway requires oxygen, and cobalt is inserted late in
the pathway; the anaerobic pathway does not require
oxygen, and cobalt insertion is the first committed step
towards cobalamin synthesis. In the aerobic pathway,
CobM catalyzes the methylation of precorrin-4 at C-11 to
yield precorrin-5. In the anaerobic pathway, CibF
catalyzes the methylation of cobalt-precorrin-4 to
cobalt-precorrin-5. Both CibF and CobM, which are
homologous, are included in this model. There are about
30 enzymes involved in vitamin B12 synthetic pathway.
The enzymes involved in the aerobic pathway are prefixed
Cob and those of the anaerobic pathway Cbi. Most of the
enzymes are shared in both pathways and several of these
enzymes are pathway-specific.
Length = 228
Score = 33.2 bits (77), Expect = 0.078
Identities = 34/135 (25%), Positives = 58/135 (42%), Gaps = 36/135 (26%)
Query: 91 GNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHKFNESQREQTVLN-- 148
G+ E IT++ R+L+ A+V++ ++G L + LL Y + + + +
Sbjct: 9 GDPELITVKGRRLLEEADVVI-----YAGSL-----VPPELLEYAR-----PDAEIYDSA 53
Query: 149 RLKQGEIVALISDA------------GTPGISDPGT--ELAKLCVDEKIPVVPIPGASAF 194
+ EI+AL+ +A G P + G E + IP +PG S+F
Sbjct: 54 SMTLEEIIALMKEAAREGKDVVRLHTGDPSLY--GAIREQMRELDALGIPYEVVPGVSSF 111
Query: 195 VAALSASGLATDEFT 209
AA +A G E T
Sbjct: 112 FAAAAALGR---ELT 123
>gnl|CDD|235577 PRK05718, PRK05718,
keto-hydroxyglutarate-aldolase/keto-deoxy-
phosphogluconate aldolase; Provisional.
Length = 212
Score = 33.3 bits (77), Expect = 0.087
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 13/61 (21%)
Query: 145 TVLNRLKQGEIVALISDAG-----TPGISDPGTELAKLCVDEKIPVVP-IPGASAFVAAL 198
TVLN E +A +AG +PG++ L K + IP++P + S + +
Sbjct: 73 TVLNP----EQLAQAIEAGAQFIVSPGLTP---PLLKAAQEGPIPLIPGVSTPSELMLGM 125
Query: 199 S 199
Sbjct: 126 E 126
>gnl|CDD|110106 pfam01081, Aldolase, KDPG and KHG aldolase. This family includes
the following members: 4-hydroxy-2-oxoglutarate aldolase
(KHG-aldolase) Phospho-2-dehydro-3-deoxygluconate
aldolase (KDPG-aldolase).
Length = 196
Score = 32.8 bits (75), Expect = 0.091
Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 14/71 (19%)
Query: 145 TVLNRLKQGEIVALISDAG-----TPGISDPGTELAKLCVDEKIPVVPIPGASAFVAALS 199
TVLN + +A ++AG +PG++ L K VD KIP+ IPG S +
Sbjct: 66 TVLNA----QQLAEAAEAGAQFVVSPGLTAD---LLKHAVDVKIPL--IPGVSTPSEIML 116
Query: 200 ASGLATDEFTF 210
L F F
Sbjct: 117 GLDLGLTRFKF 127
>gnl|CDD|180864 PRK07168, PRK07168, bifunctional uroporphyrinogen-III
methyltransferase/uroporphyrinogen-III synthase;
Reviewed.
Length = 474
Score = 32.7 bits (74), Expect = 0.17
Identities = 36/127 (28%), Positives = 58/127 (45%), Gaps = 8/127 (6%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHKF--NES 140
+YLV G+ IT +A+ LK A+++L D + L Y L+ K N
Sbjct: 5 VYLVGAGPGDEGLITKKAIECLKRADIVLY-DRLLNPFFLSYTKQTCELMYCGKMPKNHI 63
Query: 141 QREQTV----LNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAFVA 196
R++ + L K+G+IV + G P I E A+ IP +PG ++ +A
Sbjct: 64 MRQEMINAHLLQFAKEGKIVVRLK-GGDPSIFGRVGEEAETLAAANIPYEIVPGITSSIA 122
Query: 197 ALSASGL 203
A S +G+
Sbjct: 123 ASSYAGI 129
>gnl|CDD|235393 PRK05294, carB, carbamoyl phosphate synthase large subunit; Reviewed.
Length = 1066
Score = 32.4 bits (75), Expect = 0.28
Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 140 SQREQTVLNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVV-PIPGASAFVAAL 198
+ +++ +K GEI +I+ G + + ++ K+P + + GA A V A+
Sbjct: 990 HEGRPHIVDLIKNGEIDLVINTPTGRQAIRDGFSIRRAALEYKVPYITTLAGARAAVKAI 1049
Query: 199 SA 200
A
Sbjct: 1050 EA 1051
>gnl|CDD|185370 PRK15473, cbiF, cobalt-precorrin-4 C(11)-methyltransferase;
Provisional.
Length = 257
Score = 31.6 bits (72), Expect = 0.33
Identities = 35/143 (24%), Positives = 57/143 (39%), Gaps = 36/143 (25%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHKFNESQR 142
++ V G+ E ITL+ R+L+ A V++ ++G L I T LL Y
Sbjct: 10 VWFVGAGPGDKELITLKGYRLLQQAQVVI-----YAGSL-----INTELLDYCPAQAECH 59
Query: 143 EQTVLNRLKQGEIVALISDAGTPG----------------ISDPGTELAKLCVDEKIPVV 186
+ L+ +I+ L+ G I + G EL K I
Sbjct: 60 DSAELH---LEQIIDLMEAGVKAGKTVVRLQTGDVSLYGSIREQGEELTKR----GIDFQ 112
Query: 187 PIPGASAFVAALSASGLATDEFT 209
+PG S+F+ A + G+ E+T
Sbjct: 113 VVPGVSSFLGAAAELGV---EYT 132
>gnl|CDD|180320 PRK05948, PRK05948, precorrin-2 methyltransferase; Provisional.
Length = 238
Score = 31.5 bits (72), Expect = 0.36
Identities = 44/140 (31%), Positives = 63/140 (45%), Gaps = 21/140 (15%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVIL--SEDTRHSG-------KLLQYYNIKTPLLS 133
LY ++ G+ E ITL+ LR+L+SA V+ + G L IK PL
Sbjct: 6 LYGISVGPGDPELITLKGLRLLQSAPVVAFPAGLAGQPGLAEQIIAPWLSPQQIKLPLYF 65
Query: 134 YHKFNESQREQ-------TVLNRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVV 186
+ +E Q EQ V + L+QGE VA + G T LA+ + E P V
Sbjct: 66 PYVQDEEQLEQAWQAAADQVWHYLEQGEDVAFACE-GDVSFYSTFTYLAQ-TLQELYPQV 123
Query: 187 PI---PGASAFVAALSASGL 203
I PG + +AA +A G+
Sbjct: 124 AIQTIPGVCSPLAAAAALGI 143
>gnl|CDD|107321 cd06326, PBP1_STKc_like, Type I periplasmic binding domain of
uncharacterized extracellular ligand-binding proteins.
The type I periplasmic binding domain of uncharacterized
extracellular ligand-binding proteins, some of which
contain a conserved catalytic serine/threonine protein
kinase (STKc) domain in the N-terminal region. Members
of this group are sequence-similar to the branched-chain
amino acid ABC transporter
leucine-isoleucine-valine-binding protein (LIVBP); their
ligand specificity has not been determined
experimentally, however.
Length = 336
Score = 31.0 bits (71), Expect = 0.62
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 5/46 (10%)
Query: 150 LKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVV-PIPGASAF 194
++ ++ AL GTP L + +P+V P GAS+
Sbjct: 64 IEDDKVFALFGYVGTPTT----AAALPLLEEAGVPLVGPFTGASSL 105
>gnl|CDD|212119 cd10808, YdjC, Escherichia coli YdjC-like family of proteins.
Uncharacterized subfamily of YdjC-like family of
proteins. Included in this subfamily is the
uncharacterized Escherichia coli protein YdjC (also
known as ChbG), encoded by the chb
(N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel
operon, which encodes enzymes involved in growth on an
N,N'-diacetylchitobiose carbon source. The molecular
function of this subfamily is unclear.
Length = 259
Score = 30.3 bits (69), Expect = 0.83
Identities = 24/66 (36%), Positives = 29/66 (43%), Gaps = 3/66 (4%)
Query: 165 PGISDPGTELAKLCVDEKIPVVPIPGASAFVAALSASGLATDEFTFVGFLPKHARSRTER 224
PG+ D +LA IP V IP F A L+ SGL + L AR+R R
Sbjct: 135 PGVLDIVLDLAA---RYGIPAVRIPDEPPFFARLAKSGLRRRAGVGLSVLAARARARLRR 191
Query: 225 LMLSAN 230
L LS
Sbjct: 192 LGLSTP 197
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 30.6 bits (70), Expect = 0.89
Identities = 17/87 (19%), Positives = 35/87 (40%), Gaps = 13/87 (14%)
Query: 38 LLNSLSLYPKINYLLLCSCSQSQTSP---DFSNLILEQSSKRGPLEPGLYLVATPIGNLE 94
L+ SL+LY +IN +T +L++++ E +Y++ G L+
Sbjct: 444 LIKSLALYARIN-----EYGFLETPYRKVLDGSLVVDEIEYLSADEEDVYVIGQANGTLD 498
Query: 95 D---IT--LRALRVLKSANVILSEDTR 116
+ + L R S V +++
Sbjct: 499 EPGELVEELVECRRGGSGEVSVADPEG 525
>gnl|CDD|222886 PHA02577, 2, DNA end protector protein; Provisional.
Length = 181
Score = 29.8 bits (67), Expect = 1.0
Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 8/54 (14%)
Query: 206 DEFTFVGFLPKHARSRTERLMLSANEVKTQIFYVPPHKLLQFLEETSLLFGYSS 259
D F + FL +S+ LM N + Y+PP FLEE LL Y+S
Sbjct: 62 DRFPLIIFL-GSGQSKAHTLMYGLN-----LHYLPPKARQLFLEE--LLKQYAS 107
>gnl|CDD|233287 TIGR01137, cysta_beta, cystathionine beta-synthase. Members of
this family closely resemble cysteine synthase but
contain an additional C-terminal CBS domain. The
function of any bacterial member included in this family
is proposed but not proven [Amino acid biosynthesis,
Serine family].
Length = 454
Score = 30.2 bits (68), Expect = 1.0
Identities = 23/90 (25%), Positives = 33/90 (36%), Gaps = 12/90 (13%)
Query: 111 LSEDTRHSGKLLQYYNIKTPLLSYHKFNESQREQTVLNRLKQGEIVALISDAGTPG-ISD 169
L + + L QY N PL Y EQ +G++ ++ AGT G I+
Sbjct: 133 LVREIPGAHILDQYNNPSNPLAHYDGTGPEILEQC------EGKLDMFVAGAGTGGTITG 186
Query: 170 PGTELAKLCVDEKIPVVPIPGASAFVAALS 199
L E P I GA + L+
Sbjct: 187 IARYL-----KESNPKCRIVGADPEGSILA 211
>gnl|CDD|223871 COG0800, Eda, 2-keto-3-deoxy-6-phosphogluconate aldolase
[Carbohydrate transport and metabolism].
Length = 211
Score = 29.5 bits (67), Expect = 1.2
Identities = 20/64 (31%), Positives = 26/64 (40%), Gaps = 17/64 (26%)
Query: 145 TVLNRLKQGEIVALISDAG-----TPGISDPGTELAKLCVDEKIPVVPIPG---ASAFVA 196
TVLN E AG +PG++ E+AK IP IPG + +A
Sbjct: 71 TVLN----PEQARQAIAAGAQFIVSPGLNP---EVAKAANRYGIPY--IPGVATPTEIMA 121
Query: 197 ALSA 200
AL
Sbjct: 122 ALEL 125
>gnl|CDD|182774 PRK10846, PRK10846, bifunctional folylpolyglutamate synthase/
dihydrofolate synthase; Provisional.
Length = 416
Score = 30.0 bits (68), Expect = 1.3
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 183 IPVVPIPGASAFVAALSASGLATDE 207
+P VP+P A+ +AAL ASGL E
Sbjct: 250 LPNVPLPNAATALAALRASGLEVSE 274
>gnl|CDD|162241 TIGR01182, eda, Entner-Doudoroff aldolase.
2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14)
is an enzyme of the Entner-Doudoroff pathway. This
aldolase has another function, 4-hydroxy-2-oxoglutarate
aldolase (EC 4.1.3.16) shown experimentally in
Escherichia coli and Pseudomonas putida [Amino acid
biosynthesis, Glutamate family, Energy metabolism,
Entner-Doudoroff].
Length = 204
Score = 29.2 bits (66), Expect = 1.7
Identities = 22/57 (38%), Positives = 27/57 (47%), Gaps = 7/57 (12%)
Query: 145 TVLNRLKQGEIVALISDAGTPGISDPGT--ELAKLCVDEKIPVVP-IPGASAFVAAL 198
TVLN E + DAG I PG ELAK D IP++P + S + AL
Sbjct: 66 TVLNP----EQLRQAVDAGAQFIVSPGLTPELAKHAQDHGIPIIPGVATPSEIMLAL 118
>gnl|CDD|180341 PRK05990, PRK05990, precorrin-2 C(20)-methyltransferase; Reviewed.
Length = 241
Score = 29.2 bits (66), Expect = 1.8
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 83 LYLVATPIGNLEDITLRALRVLKSANVI 110
L + G+ E +TL+ALR+L++A V+
Sbjct: 5 LIGLGVGPGDPELLTLKALRLLQAAPVV 32
>gnl|CDD|215474 PLN02877, PLN02877, alpha-amylase/limit dextrinase.
Length = 970
Score = 29.7 bits (67), Expect = 1.9
Identities = 31/128 (24%), Positives = 40/128 (31%), Gaps = 20/128 (15%)
Query: 129 TPLLSYHKFNESQREQTVLNR---LKQGEIVALISD--AGTPGIS--DPGTELAKLCVDE 181
+PL N Q N G IV I D G PG+S DP + +
Sbjct: 854 SPLFRLRTANAIQERVRFHNTGPSSIPGVIVMSIEDGHEGVPGLSQLDPIYSRIVVIFNA 913
Query: 182 KIPVVPIPGASAFVAALSASGLATDEFTFVGFLPKHARSRTERLMLSANEVKTQIFYVPP 241
+ V AL L P S E + S E + +F VPP
Sbjct: 914 RPTEVSFE-----SPALKGRTLELH--------PVQVMSADEVVKKSVYEASSGVFTVPP 960
Query: 242 HKLLQFLE 249
F+E
Sbjct: 961 RTTAVFVE 968
>gnl|CDD|235289 PRK04350, PRK04350, thymidine phosphorylase; Provisional.
Length = 490
Score = 28.6 bits (65), Expect = 3.4
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 19/60 (31%)
Query: 148 NRLKQGEIVALISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAFVAALSASGLATDE 207
+L + EI A+I D V + + + SAF+ A + +GL DE
Sbjct: 92 EKLDKEEIEAIIRDI----------------VAGRYSDIEL---SAFLTASAINGLDMDE 132
>gnl|CDD|223206 COG0128, AroA, 5-enolpyruvylshikimate-3-phosphate synthase [Amino
acid transport and metabolism].
Length = 428
Score = 28.3 bits (64), Expect = 3.8
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 7/68 (10%)
Query: 186 VPIPGASAFVAAL--SASGLATDEFTFVGFLPKHARSR--TERLMLSAN---EVKTQIFY 238
+ P +S V++L A LA VG + + T ++ + E + FY
Sbjct: 163 IDGPVSSQQVSSLLLLAPLLAEGTTIIVGGVLESKPYIDHTLDMLKAFGVEVENEGYRFY 222
Query: 239 VPPHKLLQ 246
+P + L
Sbjct: 223 IPGGQKLT 230
>gnl|CDD|235696 PRK06092, PRK06092, 4-amino-4-deoxychorismate lyase; Reviewed.
Length = 268
Score = 28.3 bits (64), Expect = 4.3
Identities = 11/38 (28%), Positives = 16/38 (42%), Gaps = 6/38 (15%)
Query: 9 LMANSL----ATTGLSKTSWQSRPLLSFLRTQTLLNSL 42
+ NSL + +TS+ S L +L Q L L
Sbjct: 233 FICNSLMPVWPVRAIGETSYSSGTLTRYL--QPLCERL 268
>gnl|CDD|182064 PRK09762, PRK09762, galactosamine-6-phosphate isomerase;
Provisional.
Length = 232
Score = 27.9 bits (62), Expect = 5.1
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 3/69 (4%)
Query: 104 LKSANVILSEDTRHSGKLLQYYNIKTPLLSYHKFNESQREQTVLNRLKQGEIVALISDAG 163
+++ +L+ ++ TPLL+YH E +Q V + Q V L
Sbjct: 14 ERASEYLLAVIRSKPDAVICLATGATPLLTYHYLVEKIHQQQVD--VSQLTFVKLDEWVD 71
Query: 164 TPGISDPGT 172
P ++ PGT
Sbjct: 72 LP-LTMPGT 79
>gnl|CDD|236670 PRK10307, PRK10307, putative glycosyl transferase; Provisional.
Length = 412
Score = 28.0 bits (63), Expect = 5.4
Identities = 23/61 (37%), Positives = 28/61 (45%), Gaps = 12/61 (19%)
Query: 168 SDPGTELAKLCVDEKIPVVPIPG-ASAFVAALSASGLATDEFTFVGFLPKH---ARSRTE 223
++PGTEL +L E I V P A VAA++A LA PK AR E
Sbjct: 338 AEPGTELGQLV--EGIGVCVEPESVEALVAAIAA--LARQ----ALLRPKLGTVAREYAE 389
Query: 224 R 224
R
Sbjct: 390 R 390
>gnl|CDD|234134 TIGR03169, Nterm_to_SelD, pyridine nucleotide-disulfide
oxidoreductase family protein. Members of this protein
family include N-terminal sequence regions of (probable)
bifunctional proteins whose C-terminal sequences are
SelD, or selenide,water dikinase, the selenium donor
protein necessary for selenium incorporation into
protein (as selenocysteine), tRNA (as 2-selenouridine),
or both. However, some members of this family occur in
species that do not show selenium incorporation, and the
function of this protein family is unknown.
Length = 364
Score = 27.6 bits (62), Expect = 7.3
Identities = 21/110 (19%), Positives = 31/110 (28%), Gaps = 15/110 (13%)
Query: 102 RVLKSANVILSEDTRHSGKLLQYYNIKTPLLSYHKFNESQREQTVLNRLKQGEIVALISD 161
R L + LL + K + +L R + +
Sbjct: 166 RRLPKRGLRGQVTLIAGASLLPGFPAKV----------RRLVLRLLARRG----IEVHEG 211
Query: 162 AGTPGISDPGTELAKLCVDEKIPVVPIPGASAFVAALSASGLATDEFTFV 211
A D LA ++ GA A L+ SGL DE F+
Sbjct: 212 APVTRGPDGALILADGRTLPADAILWATGARAP-PWLAESGLPLDEDGFL 260
>gnl|CDD|188632 cd00452, KDPG_aldolase, KDPG and KHG aldolase. KDPG and KHG
aldolase. This family belongs to the class I adolases
whose reaction mechanism involves Schiff base formation
between a substrate carbonyl and lysine residue in the
active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG)
aldolase, is best known for its role in the
Entner-Doudoroff pathway of bacteria, where it catalyzes
the reversible cleavage of KDPG to pyruvate and
glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate
(KHG) aldolase, which has enzymatic specificity toward
glyoxylate, forming KHG in the presence of pyruvate, and
is capable of regulating glyoxylate levels in the
glyoxylate bypass, an alternate pathway when bacteria
are grown on acetate carbon sources.
Length = 190
Score = 27.1 bits (61), Expect = 7.4
Identities = 16/52 (30%), Positives = 21/52 (40%), Gaps = 14/52 (26%)
Query: 145 TVLNRLKQGEIVALISDAG-----TPGISDPGTELAKLCVDEKIPVVPIPGA 191
TVL E AG +PG+ DP E+ K IP+ +PG
Sbjct: 62 TVLTP----EQADAAIAAGAQFIVSPGL-DP--EVVKAANRAGIPL--LPGV 104
>gnl|CDD|202456 pfam02898, NO_synthase, Nitric oxide synthase, oxygenase domain.
Length = 366
Score = 27.4 bits (61), Expect = 8.1
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 204 ATDEFTFV----GFLPKHARSRTERLMLSANEVKTQIFYVPPHKLLQ 246
A EFT + G+ PK R L+LSAN + F +PP +L+
Sbjct: 152 ANVEFTEICIKLGWKPKRGRFDVLPLVLSANGEDPEYFELPPELVLE 198
>gnl|CDD|99740 cd00616, AHBA_syn, 3-amino-5-hydroxybenzoic acid synthase family
(AHBA_syn). AHBA_syn family belongs to pyridoxal
phosphate (PLP)-dependent aspartate aminotransferase
superfamily (fold I). The members of this CD are
involved in various biosynthetic pathways for secondary
metabolites. Some well studied proteins in this CD are
AHBA_synthase, protein product of pleiotropic regulatory
gene degT, Arnb aminotransferase and pilin
glycosylation protein. The prototype of this family, the
AHBA_synthase, is a dimeric PLP dependent enzyme.
AHBA_syn is the terminal enzyme of
3-amino-5-hydroxybenzoic acid (AHBA) formation which is
involved in the biosynthesis of ansamycin antibiotics,
including rifamycin B. Some members of this CD are
involved in 4-amino-6-deoxy-monosaccharide D-perosamine
synthesis. Perosamine is an important element in the
glycosylation of several cell products, such as
antibiotics and lipopolysaccharides of gram-positive and
gram-negative bacteria. The pilin glycosylation protein
encoded by gene pglA, is a galactosyltransferase
involved in pilin glycosylation. Additionally, this CD
consists of ArnB (PmrH) aminotransferase, a
4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying
enzyme. This CD also consists of several predicted
pyridoxal phosphate-dependent enzymes apparently
involved in regulation of cell wall biogenesis. The
catalytic lysine which is present in all characterized
PLP dependent enzymes is replaced by histidine in some
members of this CD.
Length = 352
Score = 27.5 bits (62), Expect = 8.3
Identities = 9/42 (21%), Positives = 17/42 (40%), Gaps = 2/42 (4%)
Query: 208 FTFVGFLPKHARSRTERLM--LSANEVKTQIFYVPPHKLLQF 247
+V L A + L+ L ++T++ Y P H +
Sbjct: 268 HLYVIRLDPEAGESRDELIEALKEAGIETRVHYPPLHHQPPY 309
>gnl|CDD|133152 cd05485, Cathepsin_D_like, Cathepsin_D_like, pepsin family of
proteinases. Cathepsin D is the major aspartic
proteinase of the lysosomal compartment where it
functions in protein catabolism. It is a member of the
pepsin family of proteinases. This enzyme is
distinguished from other members of the pepsin family by
two features that are characteristic of lysosomal
hydrolases. First, mature Cathepsin D is found
predominantly in a two-chain form due to a
posttranslational cleavage event. Second, it contains
phosphorylated, N-linked oligosaccharides that target
the enzyme to lysosomes via mannose-6-phosphate
receptors. Cathepsin D preferentially attacks peptide
bonds flanked by bulky hydrophobic amino acids and its
pH optimum is between pH 2.8 and 4.0. Two active site
aspartic acid residues are essential for the catalytic
activity of aspartic proteinases. Like other aspartic
proteinases, Cathepsin D is a bilobed molecule; the two
evolutionary related lobes are mostly made up of
beta-sheets and flank a deep active site cleft. Each of
the two related lobes contributes one active site
aspartic acid residue and contains a single carbohydrate
group. Cathepsin D is an essential enzyme. Mice
deficient for proteinase cathepsin D, generated by gene
targeting, develop normally during the first 2 weeks,
stop thriving in the third week and die in a state of
anorexia in the fourth week. The mice develop atrophy of
ileal mucosa followed by other degradation of intestinal
organs. In these knockout mice, lysosomal proteolysis
was normal. These results suggest that vital functions
of cathepsin D are exerted by limited proteolysis of
proteins regulating cell growth and/or tissue
homeostasis, while its contribution to bulk proteolysis
in lysosomes appears to be non-critical. This family of
aspartate proteases is classified by MEROPS as the
peptidase family A1 (pepsin A, clan AA).
Length = 329
Score = 27.1 bits (60), Expect = 8.6
Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 159 ISDAGTPGISDPGTELAKLCVDEKIPVVPIPGASAFVAALSASGLATDEFTFVG 212
I+D GT I+ P E+ KL + I PI G V + L F G
Sbjct: 214 IADTGTSLIAGPVDEIEKL--NNAIGAKPIIGGEYMVNCSAIPSLPDITFVLGG 265
>gnl|CDD|188219 TIGR02428, pcaJ_scoB_fam, 3-oxoacid CoA-transferase, B subunit.
Various members of this family are characterized as the
B subunits of succinyl-CoA:3-ketoacid-CoA transferase
(EC 2.8.3.5), beta-ketoadipate:succinyl-CoA transferase
(EC 2.8.3.6), acetyl-CoA:acetoacetate CoA transferase
(EC 2.8.3.8), and butyrate-acetoacetate CoA-transferase
(EC 2.8.3.9). This represents a very distinct clade with
strong sequence conservation within the larger family
defined by pfam01144. The A subunit represents a
different clade in pfam01144.
Length = 207
Score = 26.9 bits (60), Expect = 9.2
Identities = 23/57 (40%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 146 VLNRLKQGEIVALISDAGTPG---ISDPGTELAKLCVDEKIPVVPIPGASAFVAALS 199
V N L +G V L S+ G G +PG E L K PV +PGAS F +A S
Sbjct: 30 VANYLPEGIEVFLQSENGILGMGPAPEPGEEDPDLINAGKQPVTLLPGASYFDSADS 86
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
0.318 0.133 0.375
Gapped
Lambda K H
0.267 0.0605 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,811,212
Number of extensions: 1194146
Number of successful extensions: 1275
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1251
Number of HSP's successfully gapped: 74
Length of query: 259
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 164
Effective length of database: 6,723,972
Effective search space: 1102731408
Effective search space used: 1102731408
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 (21.7 bits)
S2: 58 (26.4 bits)