RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13219
(193 letters)
>gnl|CDD|216281 pfam01070, FMN_dh, FMN-dependent dehydrogenase.
Length = 302
Score = 162 bits (412), Expect = 1e-49
Identities = 72/192 (37%), Positives = 95/192 (49%), Gaps = 52/192 (27%)
Query: 1 MMRNVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMST 60
++R+V DRD T+LG R P GIAP+ MQ LAH DGE+A ARAA +LS +S+
Sbjct: 39 VLRDVSDRDLSTTLLGQRLSLPFGIAPTGMQGLAHPDGELALARAAAAAGIPFVLSTVSS 98
Query: 61 TSLEEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLK 120
TSLEEV A LW Q+Y+ KDR L+ +++RAE +GY A+V+T+DT VLG+R RDL+
Sbjct: 99 TSLEEVAAAAG-GPLWFQLYVPKDRELTEDLLERAEAAGYKALVLTVDTPVLGNRERDLR 157
Query: 121 NKFTMPPYLSLANFRNLKQHNEDISKFRDISAEECSSGLTDYVANQFDDSVDWDDVRSLV 180
WDD+ L
Sbjct: 158 ---------------------------------------------------TWDDLAWLR 166
Query: 181 QATKLPIVCKGI 192
K P+V KGI
Sbjct: 167 DQWKGPLVVKGI 178
>gnl|CDD|166620 PLN02979, PLN02979, glycolate oxidase.
Length = 366
Score = 160 bits (406), Expect = 3e-48
Identities = 87/189 (46%), Positives = 119/189 (62%), Gaps = 10/189 (5%)
Query: 4 NVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMSTTSL 63
+V D TVLG + P+ +AP+AMQK+AH DGE ATARAA IM LS +T+S+
Sbjct: 53 DVSKIDMTTTVLGFKISMPIMVAPTAMQKMAHPDGEYATARAASAAGTIMTLSSWATSSV 112
Query: 64 EEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLKNKF 123
EEV + P + Q+Y++K+R + Q+V+RAER+G+ AI +T+DT LG R D+KN+F
Sbjct: 113 EEVASTGPGIRFF-QLYVYKNRNVVEQLVRRAERAGFKAIALTVDTPRLGRRESDIKNRF 171
Query: 124 TMPPYLSLANFRNLKQHNEDISKFRDISAEECSSGLTDYVANQFDDSVDWDDVRSLVQAT 183
T+PP L+L NF L D+ K E SGL YVA Q D ++ W DV+ L T
Sbjct: 172 TLPPNLTLKNFEGL-----DLGKMD----EANDSGLASYVAGQIDRTLSWKDVQWLQTIT 222
Query: 184 KLPIVCKGI 192
KLPI+ KG+
Sbjct: 223 KLPILVKGV 231
>gnl|CDD|166134 PLN02493, PLN02493, probable peroxisomal (S)-2-hydroxy-acid
oxidase.
Length = 367
Score = 153 bits (387), Expect = 2e-45
Identities = 86/184 (46%), Positives = 117/184 (63%), Gaps = 10/184 (5%)
Query: 9 DSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMSTTSLEEVRA 68
D TVLG + P+ +AP+AMQK+AH DGE ATARAA IM LS +T+S+EEV +
Sbjct: 59 DMTTTVLGFKISMPIMVAPTAMQKMAHPDGEYATARAASAAGTIMTLSSWATSSVEEVAS 118
Query: 69 QNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLKNKFTMPPY 128
P + Q+Y++K+R + Q+V+RAER+G+ AI +T+DT LG R D+KN+FT+PP
Sbjct: 119 TGPGIRFF-QLYVYKNRNVVEQLVRRAERAGFKAIALTVDTPRLGRRESDIKNRFTLPPN 177
Query: 129 LSLANFRNLKQHNEDISKFRDISAEECSSGLTDYVANQFDDSVDWDDVRSLVQATKLPIV 188
L+L NF L D+ K E SGL YVA Q D ++ W DV+ L TKLPI+
Sbjct: 178 LTLKNFEGL-----DLGKMD----EANDSGLASYVAGQIDRTLSWKDVQWLQTITKLPIL 228
Query: 189 CKGI 192
KG+
Sbjct: 229 VKGV 232
>gnl|CDD|239203 cd02809, alpha_hydroxyacid_oxid_FMN, Family of homologous
FMN-dependent alpha-hydroxyacid oxidizing enzymes. This
family occurs in both prokaryotes and eukaryotes.
Members of this family include flavocytochrome b2
(FCB2), glycolate oxidase (GOX), lactate monooxygenase
(LMO), mandelate dehydrogenase (MDH), and long chain
hydroxyacid oxidase (LCHAO). In green plants, glycolate
oxidase is one of the key enzymes in photorespiration
where it oxidizes glycolate to glyoxylate. LMO catalyzes
the oxidation of L-lactate to acetate and carbon
dioxide. MDH oxidizes (S)-mandelate to phenylglyoxalate.
It is an enzyme in the mandelate pathway that occurs in
several strains of Pseudomonas which converts
(R)-mandelate to benzoate.
Length = 299
Score = 151 bits (383), Expect = 2e-45
Identities = 56/115 (48%), Positives = 78/115 (67%), Gaps = 1/115 (0%)
Query: 1 MMRNVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMST 60
++R+V RD+ T+LG + P GIAP+ +Q LAH DGE+ATARAA LS +ST
Sbjct: 45 VLRDVSKRDTSTTLLGQKLAMPFGIAPTGLQGLAHPDGELATARAAAAAGIPFTLSTVST 104
Query: 61 TSLEEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSR 115
TSLEEV A P W Q+Y+ +DR ++ +++RAE +GY A+V+T+DT VLG R
Sbjct: 105 TSLEEVAAAAP-GPRWFQLYVPRDREITEDLLRRAEAAGYKALVLTVDTPVLGRR 158
Score = 34.3 bits (80), Expect = 0.026
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 171 VDWDDVRSLVQATKLPIVCKGI 192
+ WDD+ L K P++ KGI
Sbjct: 159 LTWDDLAWLRSQWKGPLILKGI 180
>gnl|CDD|239448 cd03332, LMO_FMN, L-Lactate 2-monooxygenase (LMO) FMN-binding
domain. LMO is a FMN-containing enzyme that catalyzes
the conversion of L-lactate and oxygen to acetate,
carbon dioxide, and water. LMO is a member of the family
of alpha-hydroxy acid oxidases. It is thought to be a
homooctamer with two- and four- fold axes in the center
of the octamer.
Length = 383
Score = 150 bits (382), Expect = 2e-44
Identities = 70/205 (34%), Positives = 105/205 (51%), Gaps = 22/205 (10%)
Query: 1 MMRNVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMST 60
M+R V +RD + + G P+ +AP +Q+L H D E+ATARAA + ILS S+
Sbjct: 66 MLRGVTERDLSVELFGRTLAAPLLLAPIGVQELFHPDAELATARAAAELGVPYILSTASS 125
Query: 61 TSLEEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLK 120
+S+E+V A W Q+Y KD L+ +++RAE++GY +V+T+DT LG R RDL
Sbjct: 126 SSIEDVAAAAGDAPRWFQLYWPKDDDLTESLLRRAEKAGYRVLVVTLDTWSLGWRPRDLD 185
Query: 121 NKFTMPPYL---SLAN------FRNL--KQHNEDISKFRDI--SAEECSSGLTDYVANQF 167
+ P+L +AN FR + ED + + S +
Sbjct: 186 LGYL--PFLRGIGIANYFSDPVFRKKLAEPVGEDPEAPPPMEAAVARFVSVFSGP----- 238
Query: 168 DDSVDWDDVRSLVQATKLPIVCKGI 192
S+ W+D+ L + T LPIV KGI
Sbjct: 239 --SLTWEDLAFLREWTDLPIVLKGI 261
>gnl|CDD|215294 PLN02535, PLN02535, glycolate oxidase.
Length = 364
Score = 149 bits (379), Expect = 3e-44
Identities = 77/184 (41%), Positives = 113/184 (61%), Gaps = 13/184 (7%)
Query: 9 DSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMSTTSLEEVRA 68
D T+LG P+ IAP+AM KLAH +GE+ATARAA + IM+LS M++ ++EEV A
Sbjct: 61 DMSTTILGYTISAPIMIAPTAMHKLAHPEGEIATARAAAACNTIMVLSFMASCTVEEV-A 119
Query: 69 QNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLKNKFTMPPY 128
+ + +LQ+Y++K R ++ Q+VQRAE++GY AIV+T D LG R D+KNK P
Sbjct: 120 SSCNAVRFLQLYVYKRRDIAAQLVQRAEKNGYKAIVLTADVPRLGRREADIKNKMISP-- 177
Query: 129 LSLANFRNLKQHNEDISKFRDISAEECSSGLTDYVANQFDDSVDWDDVRSLVQATKLPIV 188
L NF L +S ++ +++ SGL + + FD S+ W D+ L T LPI+
Sbjct: 178 -QLKNFEGL------LST--EVVSDK-GSGLEAFASETFDASLSWKDIEWLRSITNLPIL 227
Query: 189 CKGI 192
KG+
Sbjct: 228 IKGV 231
>gnl|CDD|239238 cd02922, FCB2_FMN, Flavocytochrome b2 (FCB2) FMN-binding domain.
FCB2 (AKA L-lactate:cytochrome c oxidoreductase) is a
respiratory enzyme located in the intermembrane space of
fungal mitochondria which catalyzes the oxidation of
L-lactate to pyruvate. FCB2 also participates in a short
electron-transport chain involving cytochrome c and
cytochrome oxidase which ultimately directs the reducing
equivalents gained from L-lactate oxidation to oxygen,
yielding one molecule of ATP for every L-lactate
molecule consumed. FCB2 is composed of 2 domains: a
C-terminal flavin-binding domain, which includes the
active site for lacate oxidation, and an N-terminal
b2-cytochrome domain, required for efficient cytochrome
c reduction. FCB2 is a homotetramer and contains two
noncovalently bound cofactors, FMN and heme per subunit.
Length = 344
Score = 141 bits (359), Expect = 2e-41
Identities = 66/192 (34%), Positives = 102/192 (53%), Gaps = 17/192 (8%)
Query: 2 MRNVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMSTT 61
+R+V D+ T+LG + P I+P+A+ KLAH DGE+ ARAAG + ++S ++
Sbjct: 46 LRDVEKVDTSTTILGHKVSLPFFISPAALAKLAHPDGELNLARAAGKHGILQMISTNASC 105
Query: 62 SLEE-VRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLK 120
SLEE V A+ P L+ Q+Y+ KDR + ++++RAE+ G AI +T+D VLG R RD +
Sbjct: 106 SLEEIVDARPPDQPLFFQLYVNKDRTKTEELLKRAEKLGAKAIFLTVDAPVLGKRERDER 165
Query: 121 NKFTMPPYLSLANFRNLKQHNEDISKFRDISAEECSSGLTDYVANQFDDSVDWDDVRSLV 180
LK + G ++ D ++ WDD++ L
Sbjct: 166 ----------------LKAEEAVSDGPAGKKTKAKGGGAGRAMSGFIDPTLTWDDIKWLR 209
Query: 181 QATKLPIVCKGI 192
+ TKLPIV KG+
Sbjct: 210 KHTKLPIVLKGV 221
>gnl|CDD|224223 COG1304, idi, Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and
related proteins) [Coenzyme transport and metabolism].
Length = 360
Score = 128 bits (323), Expect = 7e-36
Identities = 59/192 (30%), Positives = 87/192 (45%), Gaps = 10/192 (5%)
Query: 1 MMRNVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMST 60
++ V D D T LG + P+ IAP LAH +GEV A+ A ILS + +
Sbjct: 45 VLPEVDDIDLSTTFLGQKLSAPIIIAPMTGGGLAHPEGEVINAKLAAAAGEPFILSTVGS 104
Query: 61 TSLEEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLK 120
+EEV A P Q+Y KDR + +V RA +G +V+T+D+ V G R RD
Sbjct: 105 QRIEEVAAAPP-----FQLYFSKDREFAPNLVDRAANAGAKQLVLTVDSPVGGERERDAV 159
Query: 121 NKFTMPPYLSLANFRNLKQHNEDISKFRDISAEECSSGLTDYVANQFDDSVDWDDVRSLV 180
N + P LA N+ Q E D + + +YV+ + +D +
Sbjct: 160 NGISAPA---LAIHLNVLQ--EATQPEGDRDGKGGLDSIAEYVSALSVPVISKEDGAGIS 214
Query: 181 QATKLPIVCKGI 192
+ P+V KGI
Sbjct: 215 KEWAGPLVLKGI 226
>gnl|CDD|240088 cd04737, LOX_like_FMN, L-Lactate oxidase (LOX) FMN-binding domain.
LOX is a member of the family of FMN-containing
alpha-hydroxyacid oxidases and catalyzes the oxidation
of l-lactate using molecular oxygen to generate pyruvate
and H2O2. This family occurs in both prokaryotes and
eukaryotes. Members of this family include
flavocytochrome b2 (FCB2), glycolate oxidase (GOX),
lactate monooxygenase (LMO), mandelate dehydrogenase
(MDH), and long chain hydroxyacid oxidase (LCHAO).
Length = 351
Score = 105 bits (263), Expect = 2e-27
Identities = 54/191 (28%), Positives = 90/191 (47%), Gaps = 15/191 (7%)
Query: 2 MRNVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMSTT 61
++ V D+ +LG + + P+ +AP A LAHA GEVATAR + ++ +S S T
Sbjct: 54 LQGVESPDTSTELLGIKLKTPIIMAPIAAHGLAHATGEVATARGMAEVGSLFSISTYSNT 113
Query: 62 SLEEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLKN 121
SLEE+ + W Q+Y+ KD + ++ RA+ +G AI++T D V G+R D++N
Sbjct: 114 SLEEIAKASNGGPKWFQLYMSKDDGFNRSLLDRAKAAGAKAIILTADATVGGNREADIRN 173
Query: 122 KFTMPPYLSLANFRNLKQHNEDISKFRDISAEECSSGLTDYVANQFDDSVDWDDVRSLVQ 181
KF P + N G+ + + D+ + +
Sbjct: 174 KFQFP--FGMPNLN------------HFSEGTGKGKGI-SEIYAAAKQKLSPADIEFIAK 218
Query: 182 ATKLPIVCKGI 192
+ LP++ KGI
Sbjct: 219 ISGLPVIVKGI 229
>gnl|CDD|240087 cd04736, MDH_FMN, Mandelate dehydrogenase (MDH)-like FMN-binding
domain. MDH is part of a widespread family of
homologous FMN-dependent a-hydroxy acid oxidizing
enzymes that oxidizes (S)-mandelate to phenylglyoxalate.
MDH is an enzyme in the mandelate pathway that occurs in
several strains of Pseudomonas which converts
(R)-mandelate to benzoate. This family occurs in both
prokaryotes and eukaryotes. Members of this family
include flavocytochrome b2 (FCB2), glycolate oxidase
(GOX), lactate monooxygenase (LMO), mandelate
dehydrogenase (MDH), and long chain hydroxyacid oxidase
(LCHAO).
Length = 361
Score = 98.8 bits (246), Expect = 8e-25
Identities = 64/207 (30%), Positives = 96/207 (46%), Gaps = 28/207 (13%)
Query: 4 NVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMSTTSL 63
+V RD ++ G + P+ IAP+ + +G++A ARAA +LS S S+
Sbjct: 48 DVSKRDISASLFGKVWSAPLVIAPTGLNGAFWPNGDLALARAAAKAGIPFVLSTASNMSI 107
Query: 64 EEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLKNKF 123
E+V A+ LW Q+Y+ R L+ +V+RA +GY+ +V+T D AV G R RDL+N F
Sbjct: 108 EDV-ARQADGDLWFQLYVVH-RELAELLVKRALAAGYTTLVLTTDVAVNGYRERDLRNGF 165
Query: 124 TMP--------------PYLSLANFRN----LKQHNEDISKFRDISAEECSSGLTDYVAN 165
+P P L RN L D D E + L ++
Sbjct: 166 AIPFRYTPRVLLDGILHPRWLLRFLRNGMPQLANFASD-----DAIDVEVQAAL---MSR 217
Query: 166 QFDDSVDWDDVRSLVQATKLPIVCKGI 192
Q D S +W D+R L ++ KGI
Sbjct: 218 QMDASFNWQDLRWLRDLWPHKLLVKGI 244
>gnl|CDD|131755 TIGR02708, L_lactate_ox, L-lactate oxidase. Members of this
protein oxidize L-lactate to pyruvate, reducing
molecular oxygen to hydrogen peroxide. The enzyme is
known in Aerococcus viridans, Streptococcus iniae, and
some strains of Streptococcus pyogenes where it appears
to contribute to virulence [Energy metabolism, Other].
Length = 367
Score = 96.1 bits (239), Expect = 8e-24
Identities = 43/126 (34%), Positives = 66/126 (52%)
Query: 1 MMRNVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMST 60
++++V + + + LG + + P +AP A KLA+ GEVATAR +I S ST
Sbjct: 61 LLQDVENPSTEIEFLGHKLKSPFIMAPVAAHKLANEQGEVATARGVSEFGSIYTTSSYST 120
Query: 61 TSLEEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLK 120
L E+ T W Q Y+ KD ++ ++ R + G AIV+T D V G+R D++
Sbjct: 121 ADLPEISEALNGTPHWFQFYMSKDDGINRDIMDRVKADGAKAIVLTADATVGGNREVDVR 180
Query: 121 NKFTMP 126
N F P
Sbjct: 181 NGFVFP 186
>gnl|CDD|183033 PRK11197, lldD, L-lactate dehydrogenase; Provisional.
Length = 381
Score = 80.8 bits (200), Expect = 3e-18
Identities = 60/212 (28%), Positives = 93/212 (43%), Gaps = 31/212 (14%)
Query: 2 MRNVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMSTT 61
++++ D T+ G + PV +AP + + GEV ARAA LS +S
Sbjct: 52 LKDMSDLSLETTLFGEKLSMPVALAPVGLTGMYARRGEVQAARAADAKGIPFTLSTVSVC 111
Query: 62 SLEEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLKN 121
+EEV +W Q+Y+ +DR ++RA+ +G S +V T+D V G+RYRD +
Sbjct: 112 PIEEVAPAI-KRPMWFQLYVLRDRGFMRNALERAKAAGCSTLVFTVDMPVPGARYRDAHS 170
Query: 122 KFTMPPYLSLANFRNLKQ-----------------HN-EDISKFRDISAEECSSGLTDYV 163
+ P A R Q H+ +IS + +GL DY+
Sbjct: 171 GMSGPN----AAMRRYLQAVTHPQWAWDVGLNGRPHDLGNISAYLG-----KPTGLEDYI 221
Query: 164 A---NQFDDSVDWDDVRSLVQATKLPIVCKGI 192
N FD S+ W D+ + P+V KGI
Sbjct: 222 GWLGNNFDPSISWKDLEWIRDFWDGPMVIKGI 253
>gnl|CDD|188481 TIGR03966, actino_HemFlav, heme/flavin dehydrogenase, mycofactocin
system. Members of this protein family possess an
N-terminal heme-binding domain and C-terminal
flavodehydrogenase domain, and share homology to yeast
flavocytochrome b2, to E. coli L-lactate dehydrogenase
[cytochrome], to (S)-mandelate dehydrogenase, etc. This
enzyme appears only in the context of the mycofactocin
system. Interestingly, it is absent from the four
species detected so far with mycofactocin but without an
F420 biosynthesis system.
Length = 385
Score = 73.3 bits (180), Expect = 1e-15
Identities = 38/102 (37%), Positives = 56/102 (54%), Gaps = 3/102 (2%)
Query: 7 DRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMSTTSLEEV 66
R+ TV+G PV I+P+ +Q + H DGEVA ARAA M LS ++ +EEV
Sbjct: 59 KRELSTTVMGQEISFPVLISPTGVQAV-HPDGEVAVARAAAARGTAMGLSSFASKPVEEV 117
Query: 67 RAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMD 108
A NP T + Q+Y R L ++RA +G +++T+D
Sbjct: 118 VAANPKT--FFQIYWVGSRDDILARLERARAAGAKGLILTLD 157
>gnl|CDD|132931 cd07020, Clp_protease_NfeD_1, Nodulation formation efficiency D
(NfeD) is a membrane-bound ClpP-class protease.
Nodulation formation efficiency D (NfeD; stomatin operon
partner protein, STOPP; DUF107) is a member of
membrane-anchored ClpP-class proteases. Currently, more
than 300 NfeD homologs have been identified - all of
which are bacterial or archaeal in origin. Majority of
these genomes have been shown to possess operons
containing a homologous NfeD/stomatin gene pair, causing
NfeD to be previously named STOPP (stomatin operon
partner protein). NfeD homologs can be divided into two
groups: long and short forms. Long-form homologs have a
putative ClpP-class serine protease domain while the
short form homologs do not. Downstream from the
ClpP-class domain is the so-called NfeD or DUF107
domain. N-terminal region of the NfeD homolog PH1510
(1510-N or PH1510-N) from Pyrococcus horikoshii has been
shown to possess serine protease activity and has a
Ser-Lys catalytic dyad, preferentially cleaving
hydrophobic substrates. Difference in oligomeric form
and catalytic residues between 1510-N (forming a dimer)
and ClpP (forming a tetradecamer) shows a possible
functional difference: 1510-N is likely to have a
regulatory function while ClpP is involved in protein
quality control.
Length = 187
Score = 30.2 bits (69), Expect = 0.44
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 92 VQRAERSGYSAIVITMDT 109
+ +AE G A++I +DT
Sbjct: 22 IDQAEEGGADALIIELDT 39
>gnl|CDD|233649 TIGR01945, rnfC, electron transport complex, RnfABCDGE type, C
subunit. The six subunit complex RnfABCDGE in
Rhodobacter capsulatus encodes an apparent NADH
oxidoreductase responsible for electron transport to
nitrogenase, necessary for nitrogen fixation. A closely
related complex in E. coli, RsxABCDGE (Reducer of SoxR),
reduces the 2Fe-2S-containing superoxide sensor SoxR,
active as a transcription factor when oxidized. This
family of putative NADH oxidoreductase complexes exists
in many of the same species as the related NQR, a
Na(+)-translocating NADH-quinone reductase, but is
distinct. This model describes the C subunit [Energy
metabolism, Electron transport].
Length = 435
Score = 29.6 bits (67), Expect = 0.93
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 21 CPVGIAPSAMQKLAHADGEVATARAAGMMDAI 52
CP+ + P + LA AD E A +MD I
Sbjct: 375 CPMNLLPQQLNWLALAD-EFDEAEEHNLMDCI 405
>gnl|CDD|238639 cd01314, D-HYD, D-hydantoinases (D-HYD) also called
dihydropyrimidases (DHPase) and related proteins;
DHPases are a family of enzymes that catalyze the
reversible hydrolytic ring opening of the amide bond in
five- or six-membered cyclic diamides, like
dihydropyrimidine or hydantoin. The hydrolysis of
dihydropyrimidines is the second step of reductive
catabolism of pyrimidines in human. The hydrolysis of
5-substituted hydantoins in microorganisms leads to
enantiomerically pure N-carbamyl amino acids, which are
used for the production of antibiotics, peptide
hormones, pyrethroids, and pesticides. HYDs are
classified depending on their stereoselectivity. This
family also includes collapsin response regulators
(CRMPs), cytosolic proteins involved in neuronal
differentiation and axonal guidance which have strong
homology to DHPases, but lack most of the active site
residues.
Length = 447
Score = 29.1 bits (66), Expect = 1.4
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 4/31 (12%)
Query: 41 ATARA---AGMMDA-IMILSLMSTTSLEEVR 67
ATARA A + A + I+ + S + +E+
Sbjct: 218 ATARAIRLAELAGAPLYIVHVSSKEAADEIA 248
>gnl|CDD|224305 COG1387, HIS2, Histidinol phosphatase and related hydrolases of the
PHP family [Amino acid transport and metabolism /
General function prediction only].
Length = 237
Score = 27.7 bits (62), Expect = 3.5
Identities = 18/94 (19%), Positives = 28/94 (29%), Gaps = 20/94 (21%)
Query: 86 ALSLQMVQRAERSGYSAIVIT----MDTAVLG-SRYRDLKNKFTMPPYLSLANFRNLKQH 140
A +MV+ A G I IT L + + R LK+
Sbjct: 16 ATPEEMVEAAIELGLEYIAITDHAPFLRVGLDAELLKYFIEE-----------IRELKK- 63
Query: 141 NEDISKFRDISAEECSSGLTDY---VANQFDDSV 171
DI I + G D+ + + D +
Sbjct: 64 EYDIKILIGIEVDILPDGSLDFLDEILKELDYVI 97
>gnl|CDD|137339 PRK09499, sifB, secreted effector protein SifB; Provisional.
Length = 316
Score = 27.7 bits (61), Expect = 4.0
Identities = 14/30 (46%), Positives = 21/30 (70%)
Query: 155 CSSGLTDYVANQFDDSVDWDDVRSLVQATK 184
C + LT+YVA Q +S+ +D+ SLV+ TK
Sbjct: 280 CLNELTEYVALQVHNSLFSEDLSSLVETTK 309
>gnl|CDD|240080 cd04729, NanE, N-acetylmannosamine-6-phosphate epimerase (NanE)
converts N-acetylmannosamine-6-phosphate to
N-acetylglucosamine-6-phosphate. This reaction is part
of the pathway that allows the usage of sialic acid as a
carbohydrate source. Sialic acids are a family of
related sugars that are found as a component of
glycoproteins, gangliosides, and other
sialoglycoconjugates.
Length = 219
Score = 27.2 bits (61), Expect = 4.7
Identities = 10/35 (28%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 157 SGLTDYVANQFDDSVDWDDVRSLVQATKLPIVCKG 191
SG T+ A D D++ ++ L +A +P++ +G
Sbjct: 152 SGYTEETAKTEDP--DFELLKELRKALGIPVIAEG 184
>gnl|CDD|168661 PRK06753, PRK06753, hypothetical protein; Provisional.
Length = 373
Score = 27.3 bits (61), Expect = 4.9
Identities = 7/33 (21%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 5 VCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHAD 37
V +++ + +G +GI + ++KL + D
Sbjct: 28 VFEKNESVKEVGA----GIGIGDNVIKKLGNHD 56
>gnl|CDD|173353 PTZ00057, PTZ00057, glutathione s-transferase; Provisional.
Length = 205
Score = 27.3 bits (60), Expect = 5.3
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 5/43 (11%)
Query: 108 DTAVLGSRYRDLKNKFTMPPYLSLANFRNLKQHNEDISKFRDI 150
D AV + Y D++ K+ SL NF LK HNE IS +I
Sbjct: 156 DLAVF-NLYDDIETKYPN----SLKNFPLLKAHNEFISNLPNI 193
>gnl|CDD|217238 pfam02811, PHP, PHP domain. The PHP (Polymerase and Histidinol
Phosphatase) domain is a putative phosphoesterase
domain.
Length = 174
Score = 26.8 bits (59), Expect = 6.4
Identities = 11/24 (45%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 84 DRALSLQ-MVQRAERSGYSAIVIT 106
D ALS++ +V+ A+ G AI IT
Sbjct: 13 DGALSIEELVKAAKELGLEAIAIT 36
>gnl|CDD|113793 pfam05036, SPOR, Sporulation related domain. This 70 residue
domain is composed of two 35 residue repeats found in
proteins involved in sporulation and cell division such
as FtsN, DedD, and CwlM. This domain is involved in
binding peptidoglycan. Two tandem repeats fold into a
pseudo-2-fold symmetric single-domain structure
containing numerous contacts between the repeats. FtsN
is an essential cell division protein with a simple
bitopic topology, a short N-terminal cytoplasmic segment
fused to a large carboxy periplasmic domain through a
single transmembrane domain. These repeats lay at the
periplasmic C-terminus. FtsN localises to the septum
ring complex.
Length = 75
Score = 25.4 bits (56), Expect = 6.8
Identities = 9/47 (19%), Positives = 18/47 (38%), Gaps = 2/47 (4%)
Query: 71 PSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYR 117
S ++Q+ F + A + + + G++A G YR
Sbjct: 1 ASGGYYVQLGAFSNEANAEALAAKLRAKGFAAKEAVTSGG--GGLYR 45
>gnl|CDD|213986 cd07431, PHP_PolIIIA, Polymerase and Histidinol Phosphatase domain
of alpha-subunit of bacterial polymerase III. PolIIIAs
that contain an N-terminal PHP domain have been
classified into four basic groups based on genome
composition, phylogenetic, and domain structural
analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also
called histidinol phosphatase-2/HIS2) domain is
associated with several types of DNA polymerases, such
as PolIIIA and family X DNA polymerases, stand alone
histidinol phosphate phosphatases (HisPPases), and a
number of uncharacterized protein families. DNA
polymerase III holoenzyme is one of the five eubacterial
DNA polymerases that is responsible for the replication
of the DNA duplex. The alpha subunit of DNA polymerase
III core enzyme catalyzes the reaction for polymerizing
both DNA strands. The PolIIIA PHP domain has four
conserved sequence motifs and contains an invariant
histidine that is involved in metal ion coordination,
and like other PHP structures, exhibits a distorted
(beta/alpha) 7 barrel and coordinates up to 3 metals.
Initially, it was proposed that PHP region might be
involved in pyrophosphate hydrolysis, but such activity
has not been found. It has been shown that the PHP
domain of PolIIIA has a trinuclear metal complex and is
capable of proofreading activity.
Length = 179
Score = 26.4 bits (59), Expect = 7.2
Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 90 QMVQRAERSGYSAIVITMDTAVL 112
+V RA+ GYSA+ +T D VL
Sbjct: 20 DLVARAKELGYSALALT-DRNVL 41
>gnl|CDD|216938 pfam02225, PA, PA domain. The PA (Protease associated) domain is
found as an insert domain in diverse proteases. The PA
domain is also found in a plant vacuolar sorting
receptor and members of the RZF family. It has been
suggested that this domain forms a lid-like structure
that covers the active site in active proteases, and is
involved in protein recognition in vacuolar sorting
receptors.
Length = 96
Score = 26.0 bits (57), Expect = 7.2
Identities = 6/35 (17%), Positives = 15/35 (42%)
Query: 92 VQRAERSGYSAIVITMDTAVLGSRYRDLKNKFTMP 126
+ A+R+G + ++I + + T+P
Sbjct: 50 AENAQRAGAAGVIIYNNDTGGLGGTVGDPSDVTIP 84
>gnl|CDD|234907 PRK01130, PRK01130, N-acetylmannosamine-6-phosphate 2-epimerase;
Provisional.
Length = 221
Score = 26.6 bits (60), Expect = 7.5
Identities = 8/35 (22%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 157 SGLTDYVANQFDDSVDWDDVRSLVQATKLPIVCKG 191
SG T+ + D+ ++ L++A P++ +G
Sbjct: 148 SGYTEETKKPEEP--DFALLKELLKAVGCPVIAEG 180
>gnl|CDD|223441 COG0364, Zwf, Glucose-6-phosphate 1-dehydrogenase [Carbohydrate
transport and metabolism].
Length = 483
Score = 26.8 bits (60), Expect = 9.0
Identities = 17/84 (20%), Positives = 35/84 (41%), Gaps = 14/84 (16%)
Query: 100 YSAIVITMDTAVLGSRYRDLKNKFTMPPYLSLANFRN-LKQHNE--DISKFRDISAEECS 156
Y ++ D ++G N+ FR +++ E + + EE +
Sbjct: 32 YKEGLLPEDFRIIGVARSKWSNEE----------FRALVREAIEFAKTEEIDEAVWEEFA 81
Query: 157 SGLTDYVANQFDDSVDWDDVRSLV 180
S L YV+ +DD +D+++ L+
Sbjct: 82 SRL-SYVSGDYDDPESFDELKDLL 104
>gnl|CDD|223356 COG0279, GmhA, Phosphoheptose isomerase [Carbohydrate transport and
metabolism].
Length = 176
Score = 26.1 bits (58), Expect = 9.5
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 94 RAERSGYSAIVITMDTAVL 112
ER AI ++ D++VL
Sbjct: 68 EKERPSLPAIALSTDSSVL 86
>gnl|CDD|233041 TIGR00596, rad1, DNA repair protein (rad1). All proteins in this
family for which functions are known are components in a
multiprotein endonuclease complex (usually made up of
Rad1 and Rad10 homologs). This complex is used primarily
for nucleotide excision repair but also for some aspects
of recombinational repair in some species. Most Archaeal
species also have homologs of these genes, but the
function of these Archaeal genes is not known, so we
have set our cutoff to only pick up the eukaryotic
genes.This family is based on the phylogenomic analysis
of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA
metabolism, DNA replication, recombination, and repair].
Length = 814
Score = 26.7 bits (59), Expect = 9.9
Identities = 12/60 (20%), Positives = 26/60 (43%), Gaps = 3/60 (5%)
Query: 101 SAIVITMDTAVLGS--RYRDLKNKFTMP-PYLSLANFRNLKQHNEDISKFRDISAEECSS 157
+A + D ++ D F + P ++ N+RNL++ + I + +S E +
Sbjct: 734 TAAALGSDENTTAEGLKFNDGPQDFLLKLPGVTKKNYRNLRKKVKSIRELAKLSQNELNE 793
>gnl|CDD|107204 cd01561, CBS_like, CBS_like: This subgroup includes Cystathionine
beta-synthase (CBS) and Cysteine synthase. CBS is a
unique heme-containing enzyme that catalyzes a pyridoxal
5'-phosphate (PLP)-dependent condensation of serine and
homocysteine to give cystathionine. Deficiency of CBS
leads to homocystinuria, an inherited disease of sulfur
metabolism characterized by increased levels of the
toxic metabolite homocysteine. Cysteine synthase on the
other hand catalyzes the last step of cysteine
biosynthesis. This subgroup also includes an
O-Phosphoserine sulfhydrylase found in hyperthermophilic
archaea which produces L-cysteine from sulfide and the
more thermostable O-phospho-L-serine.
Length = 291
Score = 26.3 bits (59), Expect = 9.9
Identities = 12/64 (18%), Positives = 23/64 (35%), Gaps = 18/64 (28%)
Query: 83 KDRALSLQMVQRAERSGYSAIVITMDTAVLGS-------------RYRDLKNKFTMPPYL 129
KDR +L M++ AE+ G ++ T ++ + + MP +
Sbjct: 33 KDRI-ALYMIEDAEKRG----LLKPGTTIIEPTSGNTGIGLAMVAAAKGYRFIIVMPETM 87
Query: 130 SLAN 133
S
Sbjct: 88 SEEK 91
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
0.320 0.132 0.382
Gapped
Lambda K H
0.267 0.0893 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,574,794
Number of extensions: 862365
Number of successful extensions: 986
Number of sequences better than 10.0: 1
Number of HSP's gapped: 967
Number of HSP's successfully gapped: 53
Length of query: 193
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 101
Effective length of database: 6,857,034
Effective search space: 692560434
Effective search space used: 692560434
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 (21.9 bits)
S2: 56 (25.1 bits)