RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2495
(391 letters)
>gnl|CDD|201070 pfam00191, Annexin, Annexin. This family of annexins also includes
giardin that has been shown to function as an annexin.
Length = 66
Score = 98.7 bits (247), Expect = 7e-26
Identities = 39/65 (60%), Positives = 49/65 (75%)
Query: 39 DAEVLRAAMKGFGTDEQPIIDVLAKRSNQQRQEIADAFKTLFGKDLIDDLKSELGGNFED 98
DAE+LRAAMKG GTDE +I +LA RSN Q Q I +A+K L+GKDL D+KSE G+FE
Sbjct: 2 DAELLRAAMKGLGTDEDTLIRILATRSNAQLQAIREAYKKLYGKDLEKDIKSETSGDFEK 61
Query: 99 AIVAL 103
++AL
Sbjct: 62 LLLAL 66
Score = 83.3 bits (207), Expect = 3e-20
Identities = 32/64 (50%), Positives = 46/64 (71%)
Query: 112 AKELHDAMSGVGTDEEALVEILSTLSNYGIRTIAEVYEKMYESSLEDDLKSEASGGFKRL 171
A+ L AM G+GTDE+ L+ IL+T SN ++ I E Y+K+Y LE D+KSE SG F++L
Sbjct: 3 AELLRAAMKGLGTDEDTLIRILATRSNAQLQAIREAYKKLYGKDLEKDIKSETSGDFEKL 62
Query: 172 LVSL 175
L++L
Sbjct: 63 LLAL 66
Score = 79.8 bits (198), Expect = 6e-19
Identities = 32/66 (48%), Positives = 43/66 (65%), Gaps = 1/66 (1%)
Query: 194 DAQKLLDAGVESFGTDESTFNAILVQRSYQQLRQVFKAYEKLAGHDIEEAIKSETSGSLE 253
DA+ LL A ++ GTDE T IL RS QL+ + +AY+KL G D+E+ IKSETSG E
Sbjct: 2 DAE-LLRAAMKGLGTDEDTLIRILATRSNAQLQAIREAYKKLYGKDLEKDIKSETSGDFE 60
Query: 254 DGYLSI 259
L++
Sbjct: 61 KLLLAL 66
Score = 79.4 bits (197), Expect = 9e-19
Identities = 32/66 (48%), Positives = 43/66 (65%), Gaps = 1/66 (1%)
Query: 302 DAQKLLDAGVESFGTDESTFNAILVERSYQQLRQVFKAYEKLAGHDIEEAIKSETSGSLE 361
DA+ LL A ++ GTDE T IL RS QL+ + +AY+KL G D+E+ IKSETSG E
Sbjct: 2 DAE-LLRAAMKGLGTDEDTLIRILATRSNAQLQAIREAYKKLYGKDLEKDIKSETSGDFE 60
Query: 362 DGYLSI 367
L++
Sbjct: 61 KLLLAL 66
>gnl|CDD|197661 smart00335, ANX, Annexin repeats.
Length = 53
Score = 84.8 bits (211), Expect = 7e-21
Identities = 29/53 (54%), Positives = 39/53 (73%)
Query: 51 GTDEQPIIDVLAKRSNQQRQEIADAFKTLFGKDLIDDLKSELGGNFEDAIVAL 103
GTDE+ +I++LA RSN Q Q I A+K +GKDL DD+KSE G+FE ++AL
Sbjct: 1 GTDEKTLIEILASRSNAQLQAIKQAYKKRYGKDLEDDIKSETSGDFEKLLLAL 53
Score = 73.6 bits (182), Expect = 8e-17
Identities = 26/53 (49%), Positives = 34/53 (64%)
Query: 315 GTDESTFNAILVERSYQQLRQVFKAYEKLAGHDIEEAIKSETSGSLEDGYLSI 367
GTDE T IL RS QL+ + +AY+K G D+E+ IKSETSG E L++
Sbjct: 1 GTDEKTLIEILASRSNAQLQAIKQAYKKRYGKDLEDDIKSETSGDFEKLLLAL 53
Score = 72.8 bits (180), Expect = 1e-16
Identities = 26/53 (49%), Positives = 34/53 (64%)
Query: 207 GTDESTFNAILVQRSYQQLRQVFKAYEKLAGHDIEEAIKSETSGSLEDGYLSI 259
GTDE T IL RS QL+ + +AY+K G D+E+ IKSETSG E L++
Sbjct: 1 GTDEKTLIEILASRSNAQLQAIKQAYKKRYGKDLEDDIKSETSGDFEKLLLAL 53
Score = 70.5 bits (174), Expect = 8e-16
Identities = 27/53 (50%), Positives = 40/53 (75%)
Query: 123 GTDEEALVEILSTLSNYGIRTIAEVYEKMYESSLEDDLKSEASGGFKRLLVSL 175
GTDE+ L+EIL++ SN ++ I + Y+K Y LEDD+KSE SG F++LL++L
Sbjct: 1 GTDEKTLIEILASRSNAQLQAIKQAYKKRYGKDLEDDIKSETSGDFEKLLLAL 53
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 35.3 bits (81), Expect = 0.071
Identities = 35/252 (13%), Positives = 84/252 (33%), Gaps = 28/252 (11%)
Query: 4 QQYCRFDSSLGSTYRCLFQQCLPTVVPADPFDPNGDAEVLRAAMKGFGTDEQPIIDVLAK 63
+ CRF + S + + D +P E + GT+E ++D +++
Sbjct: 946 DEVCRFVDTENSRVYGMLVAGKGRIY--DGTEPRSRIEAGPICEEERGTEESALLDEISR 1003
Query: 64 RSNQQRQEIADAFKTLFGKDLIDDL------------------KSELGGNFEDAIVALMT 105
+D F+ ++L + ++ + A+ ++
Sbjct: 1004 TILVDEYLNSDEFRM--LEELNSAVVEHGLKSPSTPVEMIINERNIVLEIGRRALDMFLS 1061
Query: 106 PLPELYAKELHDAM-SGVGTDEEALVEILSTLSNYGIRTIAEVYE---KMYESSLEDDLK 161
+P K +++ +G + I + + + +M E E K
Sbjct: 1062 NIPFGAIKSRRESLDREIGAFNNEVDGIAREEDELMFYPMFKSLKAKHRMLEEKTEYLNK 1121
Query: 162 SEASGGFKRLLVSLVQGNRDEDDEVDADAARADAQKLLDAGVESFGTDESTFNAIL-VQR 220
+ G + +L + D E D+ +++ K ++ S G D + F + L
Sbjct: 1122 ILSITGLPLISDTLRERIDTLDAEWDSFCRISESLKKYESQQVS-GLDVAQFVSFLRSVD 1180
Query: 221 SYQQLRQVFKAY 232
+ + F+ +
Sbjct: 1181 TGAFHAEYFRVF 1192
>gnl|CDD|233721 TIGR02092, glgD, glucose-1-phosphate adenylyltransferase, GlgD
subunit. This family is GlgD, an apparent regulatory
protein that appears in an alpha2/beta2 heterotetramer
with GlgC (glucose-1-phosphate adenylyltransferase,
TIGR02091) in a subset of bacteria that use GlgC for
glycogen biosynthesis [Energy metabolism, Biosynthesis
and degradation of polysaccharides].
Length = 369
Score = 32.4 bits (74), Expect = 0.38
Identities = 30/118 (25%), Positives = 43/118 (36%), Gaps = 12/118 (10%)
Query: 132 ILSTLSNYGIRTIAEVYEKMYESSLEDDLKSEASGGFKRLLVSLVQGNRDEDDEVDADAA 191
LS + N GIR + ++ SL D L S R L ++ D++
Sbjct: 40 PLSNMVNAGIRNVFIFFKNKERQSLFDHLGSGREWDLHRKRDGLFVFPYNDRDDLSEGGK 99
Query: 192 RADAQKLLDAGVESFGTDESTFNAILVQRSYQ----QLRQVFKAYEKLAGHDIEEAIK 245
R +Q L E ST +V S+ L+ V K Y + G DI K
Sbjct: 100 RYFSQNL-----EFL--KRSTSEYTVVLNSHMVCNIDLKAVLK-YHEETGKDITVVYK 149
>gnl|CDD|224866 COG1955, FlaJ, Archaeal flagella assembly protein J [Cell motility
and secretion / Intracellular trafficking and
secretion].
Length = 527
Score = 31.5 bits (72), Expect = 0.69
Identities = 30/132 (22%), Positives = 46/132 (34%), Gaps = 11/132 (8%)
Query: 45 AAMKGFGTDEQPIIDVLAKRSNQQRQEIADAFKTLFGKDLIDDLKSELGGNFEDAIVALM 104
M T + P D+ S ++ + F K I +L + G + +A +
Sbjct: 59 TYMASLSTSDIPRDDIFRILSRKEEYG---PLRKEFRK--IYNLVDKWGYSLAEACRFIA 113
Query: 105 TPLPELYAKELHDAMSGVGTDEEALVEILSTLSNYGIRTIAEVYEKMYESSLEDDLKSEA 164
P + D ++ E L E L T + YE YE +LE L
Sbjct: 114 KKTPSEILADFLDRLAYALDSGEDLKEFLER----EQDTTMDEYETEYERALE-SLD-VW 167
Query: 165 SGGFKRLLVSLV 176
+ LLVSL
Sbjct: 168 KDIYVSLLVSLT 179
>gnl|CDD|238431 cd00851, MTH1175, This uncharacterized conserved protein belongs to
a family of iron-molybdenum cluster-binding proteins
that includes NifX, NifB, and NifY, all of which are
involved in the synthesis of an iron-molybdenum cofactor
(FeMo-co) that binds the active site of the
dinitrogenase enzyme. This domain is a predicted
small-molecule-binding domain (SMBD) with an alpha/beta
fold that is present either as a stand-alone domain
(e.g. NifX and NifY) or fused to another conserved
domain (e.g. NifB) however, its function is still
undetermined.The SCOP database suggests that this domain
is most similar to structures within the ribonuclease H
superfamily. This conserved domain is represented in
two of the three major divisions of life (bacteria and
archaea).
Length = 103
Score = 29.5 bits (67), Expect = 0.95
Identities = 24/98 (24%), Positives = 35/98 (35%), Gaps = 25/98 (25%)
Query: 271 PFCNRLGVA-SFRILD---GNRDEDDEVDADAARAD-------AQKLLDAGVESFGTDES 319
G A F I D G + ++ AA A A+ L D GV
Sbjct: 13 KVSPHFGRAPYFLIYDVETGKIKNVEVIENPAAHATGGAGGKAAEFLADEGV-------- 64
Query: 320 TFNAILV----ERSYQQLRQVFKAYEKLAGHDIEEAIK 353
+ ++V R+ +LR K A +EEAI+
Sbjct: 65 --DVVIVGGIGPRALNKLRNAGIKVYKGAEGTVEEAIE 100
Score = 27.6 bits (62), Expect = 4.8
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 14/55 (25%)
Query: 195 AQKLLDAGVESFGTDESTFNAILV----QRSYQQLRQVFKAYEKLAGHDIEEAIK 245
A+ L D GV + ++V R+ +LR K A +EEAI+
Sbjct: 56 AEFLADEGV----------DVVIVGGIGPRALNKLRNAGIKVYKGAEGTVEEAIE 100
>gnl|CDD|241448 cd13294, PH_ORP_plant, Plant Oxysterol binding protein related
protein Pleckstrin homology (PH) domain. Plant ORPs
contain a N-terminal PH domain and a C-terminal
OSBP-related domain. Not much is known about its
specific function in plants to date. Members here
include: Arabidopsis, spruce, and petunia. Oxysterol
binding proteins are a multigene family that is
conserved in yeast, flies, worms, mammals and plants. In
general OSBPs and ORPs have been found to be involved in
the transport and metabolism of cholesterol and related
lipids in eukaryotes. They all contain a C-terminal
oxysterol binding domain, and most contain an N-terminal
PH domain. OSBP PH domains bind to membrane
phosphoinositides and thus likely play an important role
in intracellular targeting. They are members of the
oxysterol binding protein (OSBP) family which includes
OSBP, OSBP-related proteins (ORP), Goodpasture antigen
binding protein (GPBP), and Four phosphate adaptor
protein 1 (FAPP1). They have a wide range of purported
functions including sterol transport, cell cycle
control, pollen development and vessicle transport from
Golgi recognize both PI lipids and ARF proteins. PH
domains have diverse functions, but in general are
involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from other
PIP-binding domains by their specific high-affinity
binding to PIPs with two vicinal phosphate groups:
PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which
results in targeting some PH domain proteins to the
plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 100
Score = 29.0 bits (65), Expect = 1.2
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 252 LEDGYLSIGKMKMPEKLKTPFCNRLGVASFR 282
L+DG LS K+ P+K+K L V+S R
Sbjct: 22 LQDGVLSYYKVHGPDKVKPSGEVHLKVSSIR 52
>gnl|CDD|224709 COG1796, POL4, DNA polymerase IV (family X) [DNA replication,
recombination, and repair].
Length = 326
Score = 30.8 bits (70), Expect = 1.3
Identities = 32/159 (20%), Positives = 58/159 (36%), Gaps = 20/159 (12%)
Query: 106 PLPELYAKELHDAMSGVGTDEEALVEILSTLSNYGIRTIAEVYEKMYESSLEDDLKSEAS 165
L E+ + + G+G + + E +S + G E +K LE LK
Sbjct: 45 DLEEIEERGRLTELPGIG---KGIAEKISEYLDTGEVKKLEALKKEVPEGLEPLLKVPGL 101
Query: 166 GGFKRLLVSLVQGNRDEDDEVDADAARADAQKLLDAGVESFGTDESTFNAIL-------V 218
G K +VSL + E D + + + G+ FG + + IL
Sbjct: 102 GPKK--IVSLYK----ELGIKDLEELQEALENGKIRGLRGFG--KKSEAKILENIEFAEE 153
Query: 219 QRSYQQLRQVFKAYEKLAGH--DIEEAIKSETSGSLEDG 255
L +++ G+ ++ I++ +GSL G
Sbjct: 154 SPERIPLSFTLPIAQEIEGYLEELTPIIQASIAGSLRRG 192
>gnl|CDD|221138 pfam11573, Med23, Mediator complex subunit 23. Med23 is one of the
subunits of the Tail portion of the Mediator complex that
regulates RNA polymerase II activity. Med23 is required
for heat-shock-specific gene expression, and has been
shown to mediate transcriptional activation of E1A in
mice.
Length = 1341
Score = 30.2 bits (68), Expect = 2.1
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 95 NFEDAIVALMTPLPELYAKELHDAMSGV 122
N+ +AI +M LPE Y K LHD + V
Sbjct: 1174 NWFNAIGLIMAALPEAYWKVLHDRIIEV 1201
>gnl|CDD|218571 pfam05378, Hydant_A_N, Hydantoinase/oxoprolinase N-terminal region.
This family is found at the N-terminus of the pfam01968
family.
Length = 175
Score = 29.1 bits (66), Expect = 2.3
Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 4/64 (6%)
Query: 252 LEDGYLSIGKMKMPEKLKTPFCNRLGVASFRI-LDGNRDEDDEVDADAARADAQKLLDAG 310
LE G + + K P + V R+ DG +D +A R ++L DAG
Sbjct: 90 LEIGRQNRPDLFDLYKPLVPRELVIEVDE-RVDADGE--VIKPLDEEAVREALKELKDAG 146
Query: 311 VESF 314
VE+
Sbjct: 147 VEAV 150
Score = 28.8 bits (65), Expect = 3.1
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 181 DEDDEVDADAARADAQKLLDAGVESF 206
+ +D +A R ++L DAGVE+
Sbjct: 125 EVIKPLDEEAVREALKELKDAGVEAV 150
>gnl|CDD|224350 COG1433, COG1433, Uncharacterized conserved protein [Function
unknown].
Length = 121
Score = 28.5 bits (64), Expect = 3.1
Identities = 28/120 (23%), Positives = 41/120 (34%), Gaps = 27/120 (22%)
Query: 259 IGKMKMPEKLKTPFCNRLGVA-SFRILDGNRDEDDEVD----------ADAARADAQKLL 307
I L + G A F I+D E V+ A A+ L+
Sbjct: 3 IAIPVSDGGLDSKVSPHFGRAPYFTIVDVEDGEIKNVEVIENPAASAEKGAGIRIAELLV 62
Query: 308 DAGVESFGTDESTFNAILV----ERSYQQLRQV-FKAYEKLAGHDIEEAIKSETSGSLED 362
D GV + ++ +Y L+ K Y G +EEAIK+ G LE+
Sbjct: 63 DEGV----------DVVIASNIGPNAYNALKAAGIKVY-VAPGGTVEEAIKAFLEGELEE 111
Score = 27.3 bits (61), Expect = 6.9
Identities = 27/117 (23%), Positives = 44/117 (37%), Gaps = 27/117 (23%)
Query: 154 SSLEDDLKSEASGGFKR----LLVSLVQGNRDEDDEVDADAA-------RADAQKLLDAG 202
+ L S+ S F R +V + G + ++ AA A+ L+D G
Sbjct: 6 PVSDGGLDSKVSPHFGRAPYFTIVDVEDGEIKNVEVIENPAASAEKGAGIRIAELLVDEG 65
Query: 203 VESFGTDESTFNAILV----QRSYQQLRQV-FKAYEKLAGHDIEEAIKSETSGSLED 254
V + ++ +Y L+ K Y G +EEAIK+ G LE+
Sbjct: 66 V----------DVVIASNIGPNAYNALKAAGIKVY-VAPGGTVEEAIKAFLEGELEE 111
>gnl|CDD|235076 PRK02842, PRK02842, light-independent protochlorophyllide reductase
subunit N; Provisional.
Length = 427
Score = 29.1 bits (66), Expect = 4.6
Identities = 14/50 (28%), Positives = 20/50 (40%)
Query: 33 PFDPNGDAEVLRAAMKGFGTDEQPIIDVLAKRSNQQRQEIADAFKTLFGK 82
P P G L AA FG D + + A + R+ + + L GK
Sbjct: 242 PLGPEGTRAWLEAAAAAFGIDPDGLEEREAPAWERARKALEPYRELLRGK 291
>gnl|CDD|219182 pfam06804, Lipoprotein_18, NlpB/DapX lipoprotein. This family
consists of a number of bacterial lipoproteins often
known as NlpB or DapX. This lipoprotein is detected in
outer membrane vesicles in Escherichia coli and appears
to be nonessential.
Length = 303
Score = 29.0 bits (65), Expect = 4.7
Identities = 24/101 (23%), Positives = 38/101 (37%), Gaps = 9/101 (8%)
Query: 292 DEVDADAARADAQKLLDAGVESFGTDESTFNAILVERSYQQLRQVFKAYEKLAGHDIEEA 351
D+ D A+ A +L+ + GTD S ++ Y L Q A G I +
Sbjct: 170 DKSVRDEAQRRANELVKQIPVTMGTDRSGLPVLIARAPYNVLWQRLPAALPKMGFTITDR 229
Query: 352 IKSETSGSLEDGYLSID---WNNGG----DATEGTGAVLLG 385
+S+ G+++ Y D W G GT +G
Sbjct: 230 SQSQ--GTVKAKYAPPDDEFWQELGVKPPGLKSGTYTFQVG 268
>gnl|CDD|235239 PRK04172, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Provisional.
Length = 489
Score = 29.0 bits (66), Expect = 4.8
Identities = 27/176 (15%), Positives = 57/176 (32%), Gaps = 27/176 (15%)
Query: 36 PNGDAEVLRAAMKGFGTDEQPIIDVLAKRSNQQRQEIADAFKTLFGKDLIDDLKSELGGN 95
+ +VL+A ++ ++ LA++ + + A + L K L+ ++
Sbjct: 5 HPNEKKVLKA----LKELKEATLEELAEKLGLPPEAVMRAAEWLEEKGLV-KVEER---- 55
Query: 96 FEDAIVALMTPLPELYAKELHDAMSGVGTDEEALVEILSTLSNYGIRTIAEVYEKMYESS 155
+ + L T + YA+E G E L+ L + + E
Sbjct: 56 -VEEVYVL-TEEGKKYAEE--------GLPERRLLNALKDGGEVSLDELKEA-------L 98
Query: 156 LEDDLKSEASGGFKRL-LVSLVQGNRDEDDEVDADAARADAQKLLDAGVESFGTDE 210
L+ A G R + +G + D + L + E ++
Sbjct: 99 LDKKEVGIALGNLARKGWAKIEKGKVILKPDAYEDPEEKALKALAEGDKEELSEED 154
>gnl|CDD|223223 COG0145, HyuA, N-methylhydantoinase A/acetone carboxylase, beta
subunit [Amino acid transport and metabolism / Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 674
Score = 28.9 bits (65), Expect = 5.5
Identities = 14/53 (26%), Positives = 20/53 (37%), Gaps = 3/53 (5%)
Query: 262 MKMPEKLKTPFCNRLGVASFRILDGNRDEDDEVDADAARADAQKLLDAGVESF 314
+K P+ L P G +G +D + R A L AGVE+
Sbjct: 107 IKKPKPLV-PRVRVFGGHERVGAEGE--VIKPLDEEEVREAAAALKAAGVEAI 156
>gnl|CDD|238193 cd00316, Oxidoreductase_nitrogenase, The nitrogenase enzyme system
catalyzes the ATP-dependent reduction of dinitrogen to
ammonia. This group contains both alpha and beta
subunits of component 1 of the three known genetically
distinct types of nitrogenase systems: a
molybdenum-dependent nitrogenase (Mo-nitrogenase), a
vanadium-dependent nitrogenase (V-nitrogenase), and an
iron-only nitrogenase (Fe-nitrogenase) and, both
subunits of Protochlorophyllide (Pchlide) reductase and
chlorophyllide (chlide) reductase. The nitrogenase
systems consist of component 1 (MoFe protein, VFe
protein or, FeFe protein respectively) and, component 2
(Fe protein). The most widespread and best characterized
nitrogenase is the Mo-nitrogenase. MoFe is an
alpha2beta2 tetramer, the alternative nitrogenases are
alpha2beta2delta2 hexamers whose alpha and beta subunits
are similar to the alpha and beta subunits of MoFe. For
MoFe, each alphabeta pair contains one P-cluster (at the
alphabeta interface) and, one molecule of iron
molybdenum cofactor (FeMoco) contained within the alpha
subunit. The Fe protein contains a single [4Fe-4S]
cluster from which, electrons are transferred to the
P-cluster of the MoFe and in turn, to FeMoCo at the site
of substrate reduction. The V-nitrogenase requires an
iron-vanadium cofactor (FeVco), the iron
only-nitrogenase an iron only cofactor (FeFeco). These
cofactors are analogous to the FeMoco. The V-nitrogenase
has P clusters identical to those of MoFe. Pchlide
reductase and chlide reductase participate in the
Mg-branch of the tetrapyrrole biosynthetic pathway.
Pchlide reductase catalyzes the reduction of the D-ring
of Pchlide during the synthesis of chlorophylls (Chl)
and bacteriochlorophylls (BChl). Chlide-a reductase
catalyzes the reduction of the B-ring of Chlide-a during
the synthesis of BChl-a. The Pchlide reductase NB
complex is a an N2B2 heterotetramer resembling
nitrogenase FeMo, N and B proteins are homologous to the
FeMo alpha and beta subunits respectively. The NB
complex may serve as a catalytic site for Pchlide
reduction and, the ZY complex as a site of chlide
reduction, similar to MoFe for nitrogen reduction.
Length = 399
Score = 28.8 bits (65), Expect = 5.9
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 32 DPFDPNGDAEVLRAAMKGFGTDEQPIIDVLAKRSNQQRQEIADAFKTLFGK 82
+P LR + FG E+ + +V+A+ + +AD + L GK
Sbjct: 231 NPIGLEATDAFLRKLAELFG-IEKEVPEVIARERARLLDALADYHEYLGGK 280
>gnl|CDD|233714 TIGR02082, metH, 5-methyltetrahydrofolate--homocysteine
methyltransferase. This family represents
5-methyltetrahydrofolate--homocysteine methyltransferase
(EC 2.1.1.13), one of at least three different enzymes
able to convert homocysteine to methionine by
transferring a methyl group on to the sulfur atom. It is
also called the vitamin B12(or cobalamine)-dependent
methionine synthase. Other methionine synthases include
5-methyltetrahydropteroyltriglutamate--homocysteine
S-methyltransferase (MetE, EC 2.1.1.14, the
cobalamin-independent methionine synthase) and
betaine-homocysteine methyltransferase [Amino acid
biosynthesis, Aspartate family].
Length = 1178
Score = 29.0 bits (65), Expect = 6.1
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 143 TIAEVYEKMYESSLEDDLKSEASGG--FKRLLVSLVQGNRDEDDEVDADAAR 192
+A++YE S ++ ++E +RL +LV+G R+ +E D + AR
Sbjct: 620 ELAQLYEGTTTKSSKEAQQAEWRNLPVEERLEYALVKGEREGIEE-DLEEAR 670
>gnl|CDD|107324 cd06329, PBP1_SBP_like_3, Periplasmic solute-binding domain of
active transport proteins. Periplasmic solute-binding
domain of active transport proteins found in bacteria
and Archaea. Members of this group are initial receptors
in the process of active transport across cellular
membrane, but their substrate specificities are not
known in detail. However, they closely resemble the
group of AmiC and active transport systems for
short-chain amides and urea (FmdDEF), and thus are
likely to exhibit a ligand-binding mode similar to that
of the amide sensor protein AmiC from Pseudomonas
aeruginosa. Moreover, this binding domain has high
sequence identity to the family of hydrophobic amino
acid transporters (HAAT), and thus it may also be
involved in transport of amino acids.
Length = 342
Score = 28.4 bits (64), Expect = 6.3
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 4/41 (9%)
Query: 164 ASGGFKRLLVSLVQGNRDEDDEVDADAARADAQKLLDAGVE 204
A GG + LV+ ED++ A AQK +D GV
Sbjct: 32 AKGGVDGRPIELVE----EDNKGSPQEALRKAQKAIDDGVR 68
>gnl|CDD|237366 PRK13370, mhpB, 3-(2,3-dihydroxyphenyl)propionate dioxygenase;
Provisional.
Length = 313
Score = 28.4 bits (64), Expect = 7.2
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 12/51 (23%)
Query: 264 MPEKLKTPFCNRL---GVASFRILDGNRDEDDEVDADAARADAQKLLDAGV 311
MP PFC + V + G V +D A A A+ +LD+G+
Sbjct: 62 MP-----PFCIGVSATAVGDYGTAAGPLP----VPSDLAEALAEAVLDSGI 103
>gnl|CDD|188630 cd00408, DHDPS-like, Dihydrodipicolinate synthase family.
Dihydrodipicolinate synthase family. A member of the
class I aldolases, which use an active-site lysine which
stabilizes a reaction intermediate via Schiff base
formation, and have TIM beta/alpha barrel fold. The
dihydrodipicolinate synthase family comprises several
pyruvate-dependent class I aldolases that use the same
catalytic step to catalyze different reactions in
different pathways and includes such proteins as
N-acetylneuraminate lyase, MosA protein,
5-keto-4-deoxy-glucarate dehydratase,
trans-o-hydroxybenzylidenepyruvate hydratase-aldolase,
trans-2'-carboxybenzalpyruvate hydratase-aldolase, and
2-keto-3-deoxy- gluconate aldolase. The family is also
referred to as the N-acetylneuraminate lyase (NAL)
family.
Length = 281
Score = 28.3 bits (64), Expect = 7.3
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 181 DEDDEVDADAARADAQKLLDAGV 203
D EVD DA R + L++AGV
Sbjct: 10 TADGEVDLDALRRLVEFLIEAGV 32
Score = 28.3 bits (64), Expect = 7.3
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 289 DEDDEVDADAARADAQKLLDAGV 311
D EVD DA R + L++AGV
Sbjct: 10 TADGEVDLDALRRLVEFLIEAGV 32
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 28.6 bits (65), Expect = 7.7
Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 16/78 (20%)
Query: 114 ELHDAMSGVGTDEEALVEILSTLSNYGIRTIAEVYEKMYESSLEDDLKSEASGGFKRLLV 173
EL+D + D E + +I++ L++ GI+ V E+ +D L +E
Sbjct: 30 ELNDHLPEDIVDSEQIEDIIAMLNDMGIQ----VVEE--APDADDLLLAENEA------- 76
Query: 174 SLVQGNRDEDDEVDADAA 191
DED E +A AA
Sbjct: 77 ---DAQTDEDAEEEAAAA 91
>gnl|CDD|205895 pfam13720, Acetyltransf_11, Udp N-acetylglucosamine
O-acyltransferase; Domain 2. This is domain 2, or the
C-terminal domain, of Udp N-acetylglucosamine
O-acyltransferase. This enzyme is a zinc-dependent
enzyme that catalyzes the deacetylation of
UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine to
form UDP-3-O-(R-hydroxymyristoyl)glucosamine and
acetate.
Length = 82
Score = 26.2 bits (59), Expect = 7.7
Identities = 8/45 (17%), Positives = 18/45 (40%), Gaps = 10/45 (22%)
Query: 65 SNQQRQEIADAFKTLFGKDLIDDLKSELGGNFEDAIVALMTPLPE 109
S ++ + + A++ L+ G E+A+ L P+
Sbjct: 29 SKEEIRALKRAYRLLYRS----------GLTLEEALEELEEEAPD 63
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like; Provisional.
Length = 1195
Score = 28.3 bits (63), Expect = 9.4
Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 7/75 (9%)
Query: 126 EEALVEI----LSTLSNYGIR---TIAEVYEKMYESSLEDDLKSEASGGFKRLLVSLVQG 178
+E L+EI + +S YG R TI + Y++ +++ KR +
Sbjct: 1072 KEELLEINGLGKAKVSKYGDRLLETIESTINEYYKTDKNSSSSNDSPDSGKRRRDENINP 1131
Query: 179 NRDEDDEVDADAARA 193
N EDD+ +++
Sbjct: 1132 NVAEDDDFTKSTSQS 1146
>gnl|CDD|163676 cd07938, DRE_TIM_HMGL, 3-hydroxy-3-methylglutaryl-CoA lyase,
catalytic TIM barrel domain.
3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes
the cleavage of HMG-CoA to acetyl-CoA and acetoacetate,
one of the terminal steps in ketone body generation and
leucine degradation, and is a key enzyme in the pathway
that supplies metabolic fuel to extrahepatic tissues.
Mutations in HMGL cause a human autosomal recessive
disorder called primary metabolic aciduria that affects
ketogenesis and leucine catabolism and can be fatal due
to an inability to tolerate hypoglycemia. HMGL has a
TIM barrel domain with a catalytic center containing a
divalent cation-binding site formed by a cluster of
invariant residues that cap the core of the barrel. The
cleavage of HMG-CoA requires the presence of a divalent
cation like Mg2+ or Mn2+, and the reaction is thought to
involve general acid/base catalysis. This family
belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 274
Score = 27.7 bits (63), Expect = 9.4
Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 13/63 (20%)
Query: 183 DDEVDADAARADAQKLLDAGVESFGTDESTF-------NAILVQRSYQQLRQVFKAYEKL 235
+ EV + A++LLD G DE + V+R + + + F EKL
Sbjct: 143 EGEVPPERVAEVAERLLDLGC-----DEISLGDTIGVATPAQVRRLLEAVLERFPD-EKL 196
Query: 236 AGH 238
A H
Sbjct: 197 ALH 199
>gnl|CDD|188425 TIGR03910, pyrrolys_PylB, pyrrolysine biosynthesis radical SAM
protein. This model describes a radical SAM protein,
PylB, that is part of the three-gene cassette sufficient
for the biosynthesis of pyrrolysine (the twenty-second
amino acid) when expressed heterologously in E. coli.
The pyrrolysine next is ligated to its own tRNA and
incorporated at special UAG codons [Amino acid
biosynthesis, Other].
Length = 347
Score = 27.8 bits (62), Expect = 10.0
Identities = 32/120 (26%), Positives = 51/120 (42%), Gaps = 19/120 (15%)
Query: 157 EDDLKSEASGGFKRLLVSLVQGNRDEDDE--------VDADAARADAQKLLDAGVESFGT 208
ED GF+RL LV+ ++E VD + +KL +AG +
Sbjct: 113 EDPYYHNDPRGFERLA-ELVRMVKEETGLPVMISPGVVDNETL----KKLKEAGANWYAC 167
Query: 209 -----DESTFNAILVQRSYQQLRQVFKAYEKLAGHDIEEAIKSETSGSLEDGYLSIGKMK 263
D +N + V +S+ + R K + K G+ IEE I + +ED +S+ MK
Sbjct: 168 YQETHDRELYNKLRVGQSFDE-RMNSKRHAKRIGYLIEEGILTGVGDDIEDTAISLRGMK 226
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 0.133 0.368
Gapped
Lambda K H
0.267 0.0891 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,497,156
Number of extensions: 2081419
Number of successful extensions: 2082
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2082
Number of HSP's successfully gapped: 65
Length of query: 391
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 292
Effective length of database: 6,546,556
Effective search space: 1911594352
Effective search space used: 1911594352
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: 60 (26.6 bits)