RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10628
(238 letters)
>gnl|CDD|238103 cd00176, SPEC, Spectrin repeats, found in several proteins involved
in cytoskeletal structure; family members include
spectrin, alpha-actinin and dystrophin; the spectrin
repeat forms a three helix bundle with the second helix
interrupted by proline in some sequences; the repeats
are independent folding units; tandem repeats are found
in differing numbers and arrange in an antiparallel
manner to form dimers; the repeats are defined by a
characteristic tryptophan (W) residue in helix A and a
leucine (L) at the carboxyl end of helix C and separated
by a linker of 5 residues; two copies of the repeat are
present here.
Length = 213
Score = 118 bits (297), Expect = 7e-33
Identities = 66/197 (33%), Positives = 114/197 (57%), Gaps = 2/197 (1%)
Query: 38 ENKEAFLNNDDIGESLSGVEALLRKHKAFEKALEAQLSRIDDLEKFAKDLLAEHHYDSSG 97
KE L++ D G+ L VEALL+KH+A E L A R++ L + + L+ E H D+
Sbjct: 17 SEKEELLSSTDYGDDLESVEALLKKHEALEAELAAHEERVEALNELGEQLIEEGHPDAEE 76
Query: 98 IQQRLQAVIARKDRLKETSTARRKRLIESRQMQQFLRNMYEVGGWILQKQQICADESY-R 156
IQ+RL+ + R + L+E + RR+RL E+ +QQF R+ ++ W+ +K+ A E +
Sbjct: 77 IQERLEELNQRWEELRELAEERRQRLEEALDLQQFFRDADDLEQWLEEKEAALASEDLGK 136
Query: 157 DPTNLQSKIQKHAAFESELAANKSRVGAVTAEGESLISGGHFAA-AEIKTRLDELELEWR 215
D +++ ++KH E EL A++ R+ ++ E L+ GH A EI+ +L+EL W
Sbjct: 137 DLESVEELLKKHKELEEELEAHEPRLKSLNELAEELLEEGHPDADEEIEEKLEELNERWE 196
Query: 216 QLQESSALKRERLSDAY 232
+L E + ++++L +A
Sbjct: 197 ELLELAEERQKKLEEAL 213
Score = 74.0 bits (182), Expect = 4e-16
Identities = 42/111 (37%), Positives = 71/111 (63%), Gaps = 1/111 (0%)
Query: 128 QMQQFLRNMYEVGGWILQKQQICADESY-RDPTNLQSKIQKHAAFESELAANKSRVGAVT 186
++QQFLR+ E+ W+ +K+++ + Y D ++++ ++KH A E+ELAA++ RV A+
Sbjct: 1 KLQQFLRDADELEAWLSEKEELLSSTDYGDDLESVEALLKKHEALEAELAAHEERVEALN 60
Query: 187 AEGESLISGGHFAAAEIKTRLDELELEWRQLQESSALKRERLSDAYQTQRH 237
GE LI GH A EI+ RL+EL W +L+E + +R+RL +A Q+
Sbjct: 61 ELGEQLIEEGHPDAEEIQERLEELNQRWEELRELAEERRQRLEEALDLQQF 111
Score = 40.1 bits (94), Expect = 4e-04
Identities = 35/118 (29%), Positives = 56/118 (47%), Gaps = 30/118 (25%)
Query: 11 KEAFLNNDDIGESLSGVEALLRKHKAFENKEAFLNNDDIGESLSGVEALLRKHKAFEKAL 70
KEA L ++D+G+ L VE LL+KHK E + L
Sbjct: 125 KEAALASEDLGKDLESVEELLKKHKELEEE-----------------------------L 155
Query: 71 EAQLSRIDDLEKFAKDLLAEHHYDSSG-IQQRLQAVIARKDRLKETSTARRKRLIESR 127
EA R+ L + A++LL E H D+ I+++L+ + R + L E + R+K+L E+
Sbjct: 156 EAHEPRLKSLNELAEELLEEGHPDADEEIEEKLEELNERWEELLELAEERQKKLEEAL 213
>gnl|CDD|197544 smart00150, SPEC, Spectrin repeats.
Length = 101
Score = 75.1 bits (185), Expect = 1e-17
Identities = 41/100 (41%), Positives = 66/100 (66%), Gaps = 1/100 (1%)
Query: 130 QQFLRNMYEVGGWILQKQQICADESY-RDPTNLQSKIQKHAAFESELAANKSRVGAVTAE 188
QQFLR+ E+ W+ +K+Q+ A E +D ++++ ++KH AFE+EL A++ RV A+
Sbjct: 1 QQFLRDADELEAWLEEKEQLLASEDLGKDLESVEALLKKHEAFEAELEAHEERVEALNEL 60
Query: 189 GESLISGGHFAAAEIKTRLDELELEWRQLQESSALKRERL 228
GE LI GH A EI+ RL+EL W +L+E + +R++L
Sbjct: 61 GEQLIEEGHPDAEEIEERLEELNERWEELKELAEERRQKL 100
Score = 68.9 bits (169), Expect = 2e-15
Identities = 36/86 (41%), Positives = 56/86 (65%)
Query: 38 ENKEAFLNNDDIGESLSGVEALLRKHKAFEKALEAQLSRIDDLEKFAKDLLAEHHYDSSG 97
E KE L ++D+G+ L VEALL+KH+AFE LEA R++ L + + L+ E H D+
Sbjct: 15 EEKEQLLASEDLGKDLESVEALLKKHEAFEAELEAHEERVEALNELGEQLIEEGHPDAEE 74
Query: 98 IQQRLQAVIARKDRLKETSTARRKRL 123
I++RL+ + R + LKE + RR++L
Sbjct: 75 IEERLEELNERWEELKELAEERRQKL 100
>gnl|CDD|215918 pfam00435, Spectrin, Spectrin repeat. Spectrin repeat-domains are
found in several proteins involved in cytoskeletal
structure. These include spectrin, alpha-actinin and
dystrophin. The sequence repeat used in this family is
taken from the structural repeat in reference. The
spectrin domain- repeat forms a three helix bundle. The
second helix is interrupted by proline in some
sequences. The repeats are defined by a characteristic
tryptophan (W) residue at position 17 in helix A and a
leucine (L) at 2 residues from the carboxyl end of helix
C. Although the domain occurs in ultiple repeats along
sequences, the domains are actually stable on their own
- ie they act, biophysically, like domains rather than
repeats that along function when aggregated.
Length = 105
Score = 74.3 bits (183), Expect = 3e-17
Identities = 40/105 (38%), Positives = 69/105 (65%), Gaps = 1/105 (0%)
Query: 127 RQMQQFLRNMYEVGGWILQKQQICADESY-RDPTNLQSKIQKHAAFESELAANKSRVGAV 185
+QQF R+ ++ WI +K+ + + E Y +D ++Q+ ++KH A E+ELAA++ RV A+
Sbjct: 1 LLLQQFFRDADDLESWIEEKEALLSSEDYGKDLESVQALLKKHKALEAELAAHQDRVEAL 60
Query: 186 TAEGESLISGGHFAAAEIKTRLDELELEWRQLQESSALKRERLSD 230
E LI+ GH+A+ EI+ RL+EL W QL E +A ++++L +
Sbjct: 61 NELAEKLIAEGHYASEEIQERLEELNERWEQLLELAAERKQKLEE 105
Score = 68.1 bits (167), Expect = 6e-15
Identities = 37/86 (43%), Positives = 57/86 (66%)
Query: 38 ENKEAFLNNDDIGESLSGVEALLRKHKAFEKALEAQLSRIDDLEKFAKDLLAEHHYDSSG 97
E KEA L+++D G+ L V+ALL+KHKA E L A R++ L + A+ L+AE HY S
Sbjct: 18 EEKEALLSSEDYGKDLESVQALLKKHKALEAELAAHQDRVEALNELAEKLIAEGHYASEE 77
Query: 98 IQQRLQAVIARKDRLKETSTARRKRL 123
IQ+RL+ + R ++L E + R+++L
Sbjct: 78 IQERLEELNERWEQLLELAAERKQKL 103
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 31.8 bits (73), Expect = 0.24
Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 4/70 (5%)
Query: 27 VEALLRKHKAFENKEAFLNNDDIGESLSGVEALLRKHKAFEKALEAQLSRIDDLEKFAKD 86
E + +K + + +G LS A+L+ E+ L+ +I DL +
Sbjct: 28 KEEVYKKIPEIAEIDDEIA--KLGIKLS--RAILKNPDKKEETLKELKEKITDLRVKKAE 83
Query: 87 LLAEHHYDSS 96
LL + Y
Sbjct: 84 LLVSNGYPPD 93
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 31.2 bits (71), Expect = 0.59
Identities = 30/190 (15%), Positives = 66/190 (34%), Gaps = 7/190 (3%)
Query: 47 DDIGESLSGVEALLRKHKAFEKALEAQLSRIDDLEKFAKDLLAEHHYDSSGIQQRLQAVI 106
+++ +S + L + +A + LE +++++ + + E ++ L
Sbjct: 722 EELSRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAE 781
Query: 107 ARKDRLKETSTARRKRLIESRQMQQFLRNMYEVGGWILQKQQICADESYRDPTNLQSKIQ 166
A + L+ ++ L R+ LR L A +L+ +I
Sbjct: 782 AEIEELEAQIEQLKEELKALREALDELRA-------ELTLLNEEAANLRERLESLERRIA 834
Query: 167 KHAAFESELAANKSRVGAVTAEGESLISGGHFAAAEIKTRLDELELEWRQLQESSALKRE 226
+L + + I E+++ L+ L E L+E+ AL R
Sbjct: 835 ATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELESELEALLNERASLEEALALLRS 894
Query: 227 RLSDAYQTQR 236
L + + R
Sbjct: 895 ELEELSEELR 904
Score = 30.8 bits (70), Expect = 0.65
Identities = 30/184 (16%), Positives = 70/184 (38%), Gaps = 10/184 (5%)
Query: 50 GESLSGVEALLRKHKAFEKALEAQLSRIDDLEKFAKDLLAEHHYDSSGIQQRLQAVIARK 109
G+ + + ++ + I++LE+ ++L + I + +A+ +
Sbjct: 652 GDLVRPGGVITGGSAKTNSSILERRREIEELEEKIEELEEK-------IAELEKALAELR 704
Query: 110 DRLKETSTARRKRLIESRQMQQFLRNMYEVGGWILQKQQICADESYR---DPTNLQSKIQ 166
L+E + E ++ + + + + + + + + + + T L+++I+
Sbjct: 705 KELEELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIE 764
Query: 167 KHAAFESELAANKSRVGAVTAEGESLISGGHFAAAEIKTRLDELELEWRQLQESSALKRE 226
+ E + A E E+ I ++ LDEL E L E +A RE
Sbjct: 765 ELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRE 824
Query: 227 RLSD 230
RL
Sbjct: 825 RLES 828
>gnl|CDD|235658 PRK05972, ligD, ATP-dependent DNA ligase; Reviewed.
Length = 860
Score = 30.6 bits (70), Expect = 0.80
Identities = 17/58 (29%), Positives = 22/58 (37%), Gaps = 7/58 (12%)
Query: 69 ALEAQLS--RIDDLEKFAKDLLAEHHYDSSGIQQRLQAVIARKDRLKETSTARRKRLI 124
AL+ R +DL FA DL D R + R+ RL+ A R I
Sbjct: 319 ALQNAFDEGRTEDLVYFAFDLPFLGGED-----LRELPLEERRARLRALLEAARSDRI 371
>gnl|CDD|216274 pfam01062, Bestrophin, Bestrophin, RFP-TM, chloride channel.
Bestrophin is a 68-kDa basolateral plasma membrane
protein expressed in retinal pigment epithelial cells
(RPE). It is encoded by the VMD2 gene, which is mutated
in Best macular dystrophy, a disease characterized by a
depressed light peak in the electrooculogram. VMD2
encodes a 585-amino acid protein with an approximate
mass of 68 kDa which has been designated bestrophin.
Bestrophin shares homology with the Caenorhabditis
elegans RFP gene family, named for the presence of a
conserved arginine (R), phenylalanine (F), proline (P),
amino acid sequence motif. Bestrophin is a plasma
membrane protein, localised to the basolateral surface
of RPE cells consistent with a role for bestrophin in
the generation or regulation of the EOG light peak.
Bestrophin and other RFP family members represent a new
class of chloride channels, indicating a direct role for
bestrophin in generating the light peak. The VMD2 gene
underlying Best disease was shown to represent the first
human member of the RFP-TM protein family. More than 97%
of the disease-causing mutations are located in the
N-terminal RFP-TM domain implying important functional
properties. The bestrophins are four-pass transmembrane
chloride-channel proteins, and the RFP-TM or bestrophin
domain extends from the N-terminus through approximately
350 amino acids and contains all of the TM domains as
well as nearly all reported disease causing mutations.
Interestingly, the RFP motif is not conserved
evolutionarily back beyond Metazoa, neither is it in
plant members.
Length = 284
Score = 29.4 bits (67), Expect = 1.3
Identities = 20/85 (23%), Positives = 31/85 (36%), Gaps = 12/85 (14%)
Query: 57 EALLRKHKAFEKALEAQLSRIDDLEKFAKDLLAEHHYDSSGIQQRLQAVIARKDRL---- 112
LLR+ A+ AL A L I + LL+E ++L L
Sbjct: 111 RRLLRRTIAYAHALRALLRGISPAVD-LEHLLSEEEE------EKLLQSSNPPYALLIVW 163
Query: 113 -KETSTARRKRLIESRQMQQFLRNM 136
+ ARR+ I+ Q+ Q +
Sbjct: 164 AASLAKARREGRIDDIQLVQLDEEL 188
>gnl|CDD|214697 smart00498, FH2, Formin Homology 2 Domain. FH proteins control
rearrangements of the actin cytoskeleton, especially in
the context of cytokinesis and cell polarisation.
Members of this family have been found to interact with
Rho-GTPases, profilin and other actin-assoziated
proteins. These interactions are mediated by the
proline-rich FH1 domain, usually located in front of FH2
(but not listed in SMART). Despite this cytosolic
function, vertebrate formins have been assigned
functions within the nucleus. A set of Formin-Binding
Proteins (FBPs) has been shown to bind FH1 with their WW
domain.
Length = 392
Score = 29.6 bits (67), Expect = 1.4
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 13/88 (14%)
Query: 27 VEALLRK--HKAFENKEAFLNNDDIGESLSGVEALLR------KHKAFEKALEAQLSRID 78
+ LLRK E KEA L D+ S+ +E LL+ + K + E +
Sbjct: 85 LAILLRKLHMSYEEIKEAILEGDEDVLSVDLLEQLLKYAPTKEELKKLREYKEEDPEELA 144
Query: 79 DLEKFAKDLLAEHHYDSSGIQQRLQAVI 106
E+F + + ++RL A++
Sbjct: 145 RAEQFLLLISNIPYL-----EERLNALL 167
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 29.9 bits (67), Expect = 1.4
Identities = 32/176 (18%), Positives = 69/176 (39%), Gaps = 34/176 (19%)
Query: 56 VEALLRKHKAFEKALEAQLSRIDDLEKFAKDLLAEHHYDSSGIQQRLQAVIARKDRLKET 115
++A L++ + E L Q+S + LE+ K L + ++ +Q +L ++++ K + K++
Sbjct: 418 LQAELQQARQNESELRNQISLLTSLERSLKSDLGQLKKENDMLQTKLNSMVSAKQKDKQS 477
Query: 116 STARRKRLIESRQMQQFLRNMYEVGGWILQKQQICADESYRDPTNLQSKIQKHAAFESEL 175
+ KRL + ++Q+ ++ + E E
Sbjct: 478 MQSMEKRLKSEADSRVNA------------EKQLAEEKKRKK--------------EEEE 511
Query: 176 AANKSRVGAVTAEGESLISGGHFAAAEIKTRLDELELEWRQLQESSALKRERLSDA 231
A ++ A + E A +K +LE+E ++L+ LK E
Sbjct: 512 TAARAAAQAAASREEC--------AESLKQAKQDLEMEIKKLEHDLKLKEEECRML 559
>gnl|CDD|130695 TIGR01634, tail_P2_I, phage tail protein, P2 protein I family.
This model represents the family of phage P2 protein I
and related tail proteins from a number of temperate
phage of Gram-negative bacteria. This model is built as
a fragment model and identifies some phage tail proteins
with strong but local similarity to members of the seed
alignment [Mobile and extrachromosomal element
functions, Prophage functions].
Length = 139
Score = 28.7 bits (64), Expect = 1.5
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 220 SSALKRERLSDAYQTQRHK 238
+KR+ + AY RHK
Sbjct: 57 PEKVKRDVIRSAYFIHRHK 75
>gnl|CDD|150280 pfam09551, Spore_II_R, Stage II sporulation protein R
(spore_II_R). SpoIIR is designated stage II
sporulation protein R. A comparative genome analysis of
all sequenced genomes of Firmicutes shows that the
proteins are strictly conserved among the sub-set of
endospore-forming species. SpoIIR is a signalling
protein that links the activation of sigma E to the
transcriptional activity of sigma F during sporulation.
Length = 132
Score = 28.3 bits (64), Expect = 1.8
Identities = 9/39 (23%), Positives = 19/39 (48%)
Query: 56 VEALLRKHKAFEKALEAQLSRIDDLEKFAKDLLAEHHYD 94
+ L K+ E+A + ++E+ A+ ++ E YD
Sbjct: 34 LTPKLEDSKSIEEARRVIKENLPEIEEIAEKVIKEEGYD 72
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 29.2 bits (66), Expect = 1.9
Identities = 36/184 (19%), Positives = 74/184 (40%), Gaps = 23/184 (12%)
Query: 47 DDIGESLSGVEALLRKHKAFEKALEAQLSRIDDLEKFAKDLLAEHHYDSSGIQQRLQAVI 106
++ E + +EA L + + +E +L R +DL + + +++R + +
Sbjct: 471 EEDRERVEELEAELEDLEEEVEEVEERLERAEDLVEAEDRI--------ERLEERREDLE 522
Query: 107 ARKDRLKETSTARRKRLIESRQMQQFLRNMYEVGGWILQKQQICADESYRDPTNLQSKIQ 166
+ET +R+R E R+ L E + + A+E +
Sbjct: 523 ELIAERRETIEEKRERAEELRERAAELEAEAEEKREAAAEAEEEAEE----------ARE 572
Query: 167 KHAAFESELAANKSRVGAVTAEGESLISGGHFAAAEIKTRLDELELEWRQLQESSALKRE 226
+ A S+LA K R+ ++ L A A+ + ++ L + L E + +RE
Sbjct: 573 EVAELNSKLAELKERIESLERIRTLLA-----AIADAEDEIERLREKREALAELNDERRE 627
Query: 227 RLSD 230
RL++
Sbjct: 628 RLAE 631
>gnl|CDD|220506 pfam09989, DUF2229, CoA enzyme activase uncharacterized domain
(DUF2229). Members of this family include various
bacterial hypothetical proteins, as well as CoA enzyme
activases. The exact function of this domain has not, as
yet, been defined.
Length = 218
Score = 28.7 bits (65), Expect = 2.0
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 7/57 (12%)
Query: 37 FENKEAFLNN-DDIGESL--SGVEALLRKHKAFEKALEAQLSRIDDLEKFAKDLLAE 90
++KEA ++G+ L S E KA EKALE Q + DL K ++ LA
Sbjct: 122 LKDKEALAKRLYELGKKLGISKEEI----KKAVEKALEEQEAFKKDLRKKGEEALAY 174
>gnl|CDD|234713 PRK00283, xerD, site-specific tyrosine recombinase XerD; Reviewed.
Length = 299
Score = 29.0 bits (66), Expect = 2.2
Identities = 22/58 (37%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 79 DLEKFAKDLLAEHHYDSSGIQQR-LQAVIA--RKDRLKETSTARRKRLIESRQMQQFL 133
DLE FA + LA + + LQA +A + K TS+AR RL R+ QFL
Sbjct: 33 DLELFA-EWLAARGLSLAEATRDDLQAFLAELAEGGYKATSSAR--RLSALRRFFQFL 87
>gnl|CDD|227778 COG5491, VPS24, Conserved protein implicated in secretion [Cell
motility and secretion].
Length = 204
Score = 28.2 bits (63), Expect = 2.8
Identities = 20/81 (24%), Positives = 30/81 (37%), Gaps = 1/81 (1%)
Query: 59 LLRKHKAFEKALEAQLSRIDDLEKFAKDLLAEHHYDSSGIQQRLQAVIARKDRLKETSTA 118
L+R+ K K + L+ I + LAE Y + RL A I+R L
Sbjct: 12 LVRELKQEAKKGQVLLNEIAKKAPNRR-RLAEELYKLRKARSRLDASISRLQSLDTMLFE 70
Query: 119 RRKRLIESRQMQQFLRNMYEV 139
+ S M + M E+
Sbjct: 71 KVVMRQVSGDMAKAAMYMNEL 91
>gnl|CDD|183280 PRK11701, phnK, phosphonate C-P lyase system protein PhnK;
Provisional.
Length = 258
Score = 28.4 bits (64), Expect = 3.1
Identities = 17/39 (43%), Positives = 19/39 (48%), Gaps = 14/39 (35%)
Query: 71 EAQLSRIDDLEK-FAKDLLAEHHYDSSGIQQRLQAVIAR 108
E +RIDDL F S G+QQRLQ IAR
Sbjct: 139 EIDAARIDDLPTTF-----------SGGMQQRLQ--IAR 164
>gnl|CDD|176256 cd08296, CAD_like, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family, reduce
cinnamaldehydes to cinnamyl alcohols in the last step of
monolignal metabolism in plant cells walls. CAD binds 2
zinc ions and is NADPH- dependent. CAD family members
are also found in non-plant species, e.g. in yeast where
they have an aldehyde reductase activity. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADHs), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 333
Score = 28.4 bits (64), Expect = 3.4
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 74 LSRIDDLEKFAKDLLAEHHYDSS--GIQQRLQA 104
+SR D A+ L A H+ D+S + + LQ
Sbjct: 193 ISRGSDKADLARKLGAHHYIDTSKEDVAEALQE 225
>gnl|CDD|131350 TIGR02297, HpaA, 4-hydroxyphenylacetate catabolism regulatory
protein HpaA. This putative transcriptional regulator,
which contains both the substrate-binding, dimerization
domain (pfam02311) and the helix-turn-helix DNA-binding
domain (pfam00165) of the AraC famil, is located
proximal to genes of the 4-hydroxyphenylacetate
catabolism pathway.
Length = 287
Score = 28.2 bits (63), Expect = 4.0
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 121 KRLIESRQMQQFLRNMYEVGGWILQKQQICADESYRDP 158
KRLI R MQ+ R + I QI D Y+DP
Sbjct: 232 KRLIIERVMQEARRLLLFTQHSI---NQIAYDLGYKDP 266
>gnl|CDD|237365 PRK13369, PRK13369, glycerol-3-phosphate dehydrogenase;
Provisional.
Length = 502
Score = 27.6 bits (62), Expect = 6.3
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 3/40 (7%)
Query: 195 GGHFAAAEIKTRLDELELEWRQLQESSALKRERLSDAYQT 234
GG A A+ T D+L + L A R + Y T
Sbjct: 393 GGDIANADFDTFADDLRDRYPWLPRPLA---HRYARLYGT 429
>gnl|CDD|176469 cd01597, pCLME, prokaryotic 3-carboxy-cis,cis-muconate
cycloisomerase (CMLE)_like. This subgroup contains
pCLME and related proteins, and belongs to the Lyase
class I family. Members of this family for the most part
catalyze similar beta-elimination reactions in which a
C-N or C-O bond is cleaved with the release of fumarate
as one of the products. These proteins are active as
tetramers. The four active sites of the homotetrameric
enzyme are each formed by residues from three different
subunits. CMLE catalyzes the cyclization of
3-carboxy-cis,cis-muconate (3CM) to
4-carboxy-muconolactone in the beta-ketoadipate pathway.
This pathway is responsible for the catabolism of a
variety of aromatic compounds into intermediates of the
citric cycle in prokaryotic and eukaryotic
micro-organisms.
Length = 437
Score = 27.6 bits (62), Expect = 6.7
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 10/62 (16%)
Query: 162 QSKIQKHAAFESELAANKSRVGAVTAEGESLISGGHFAAAEIKTRLDELELEWRQLQESS 221
++++Q E+ LA ++ +G + E AAAEI D L+ L E++
Sbjct: 18 ENRVQAMLDVEAALARAQAELGVIPKE----------AAAEIAAAADVERLDLEALAEAT 67
Query: 222 AL 223
A
Sbjct: 68 AR 69
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 26.9 bits (60), Expect = 7.1
Identities = 23/109 (21%), Positives = 47/109 (43%), Gaps = 10/109 (9%)
Query: 27 VEALLRKHKAFENKEAFLN--NDDIGESLSGVEALLRKHKAFEKALEAQLSRIDDLEKFA 84
+ L ++ + + A L ++ + ++ L +A + L+ +L+RI L A
Sbjct: 68 LPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLSANA 127
Query: 85 KDLLAEHHYDSSGIQQRLQAVIARKDRLKETSTARRKRLIESRQMQQFL 133
+L E+ + L+ +A + E A +RL E+ Q + FL
Sbjct: 128 IELDEEN--------RELREELAELKQENEALEAENERLQENEQRRWFL 168
>gnl|CDD|184905 PRK14941, PRK14941, DNA polymerase III subunit beta; Provisional.
Length = 374
Score = 27.0 bits (60), Expect = 9.4
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 10/55 (18%)
Query: 124 IESRQMQQFLRNMYEVG-GWILQKQQ--------ICADE-SYRDPTNLQSKIQKH 168
I +R +Q FLR+MY+ + +++Q+ I D+ Y+ P +SK +K
Sbjct: 69 IRARTLQDFLRSMYDTEVTFSIERQEISDHGTVHIATDKGRYKIPCLFESKPEKQ 123
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
0.313 0.129 0.347
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,200,632
Number of extensions: 1181299
Number of successful extensions: 1368
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1329
Number of HSP's successfully gapped: 132
Length of query: 238
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 144
Effective length of database: 6,768,326
Effective search space: 974638944
Effective search space used: 974638944
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: 57 (25.7 bits)