RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780375|ref|YP_003064788.1| hypothetical protein
CLIBASIA_01300 [Candidatus Liberibacter asiaticus str. psy62]
(175 letters)
>gnl|CDD|33143 COG3334, COG3334, Uncharacterized conserved protein [Function
unknown].
Length = 192
Score = 94.3 bits (234), Expect = 1e-20
Identities = 41/144 (28%), Positives = 78/144 (54%), Gaps = 5/144 (3%)
Query: 26 FLQGFANQSYGDPTLVDREIQQYCTNVIDSVRERDYLSQKKVLEDLQK--DIEQRVILLE 83
+ A + EI+++C N+ D+ ++ Y QK++LE L+ ++ +R+ LE
Sbjct: 38 EAEDAAAELAEKKAAAQSEIEKFCANIADAAADQLYALQKELLEKLKDLAEVNERLKALE 97
Query: 84 NHKKEYNLWFQKYDSFIMSYNK---NILDIYKKMDSDSAALQLEQIDPDISSHILMRLSP 140
K E ++ + + S ++ IY KM D+AA LE + + ++ ILM+L P
Sbjct: 98 KKKAELKDLEEEREGILRSKQAEDGKLVKIYSKMKPDAAAAILENLPDEEAAAILMKLKP 157
Query: 141 RQSSLIMSKMNPKSATMITNVVAN 164
R+ LI++KM+P+ A +T ++A+
Sbjct: 158 RKLGLILAKMDPEKAATLTELIAS 181
>gnl|CDD|58628 cd03687, Dehydratase_LU, Dehydratase large subunit. This family
contains the large (alpha) subunit of B12-dependent
glycerol dehydratases (GDHs) and B12-dependent diol
dehydratases (DDHs). GDH is isofunctional with DDH.
These enzymes can each catalyze the conversion of
1,2-propanediol, glycerol, and 1,2-ethanediol to the
corresponding aldehydes via a coenzyme B12
(adenosylcobalamin)-dependent radical mechanism. Both
enzymes exhibit a subunit composition of
alpha2beta2gamma2. The enzymes differ in substrate
specificity; glycerol is the preferred substrate for GDH
and 1,2-propanediol for DDH. GDH shows almost equal
affinity for both (R) and (S)-isomers while DDH prefers
the (S) isomer. GDH plays a key role in the
dihydroxyacetone (DHA) pathway and DDH in the anaerobic
degradation of 1,2-diols. The radical mechanism has been
well studied for Klebsiella oxytoca DDH and involves
binding of 1,2-propanediol to the enzyme to induce
hemolytic cleavage of the Co-C5' bond of the coenzyme to
form cob(II)alamin and the adenosyl radical. Hydrogen
abstraction from the substrate follows producing a
substrate generated radical and 5'-deoxyadenosine.
Rearrangement to the product radical is then followed by
abstraction of a hydrogen atom from 5'-deoxyadenosine to
produce the hydrated propionaldehyde and regenerate the
adenosyl radical. After the Co-C5' bond is reformed and
the hydrated aldehyde dehydrated, the process is
complete. GDH has a higher affinity for coenzyme B12
than DDH. Both GDH and DDH are activated by various
monovalent cations with K+, NH4+, and Rb+ being the most
effective. However, DDH differs from GDH in that it is
partially active with Cs+ and Na+. In general, the alpha
and beta subunits for both enzymes are on different
chains. However, for a subset of the GDHs, alpha and
beta subunits appear to be on a single chain..
Length = 545
Score = 31.1 bits (70), Expect = 0.16
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 93 FQKYDSFIMSYNKNILDIYKKMDSDSAALQLEQIDPDISSHILMRL----SPRQSSLIMS 148
F D FI Y N+ + M DS L +DP++ ++RL +P + ++S
Sbjct: 52 FDMIDHFIARYGINLERAEEAMALDSVKLARMLVDPNVPREEIVRLTTAMTPAKLVEVVS 111
Query: 149 KMNPKSATM 157
+MN M
Sbjct: 112 QMNVVEMMM 120
>gnl|CDD|35482 KOG0261, KOG0261, KOG0261, RNA polymerase III, large subunit
[Transcription].
Length = 1386
Score = 29.5 bits (66), Expect = 0.54
Identities = 24/96 (25%), Positives = 41/96 (42%), Gaps = 6/96 (6%)
Query: 74 DIEQRVILLENHKKEYNLWFQKYDSFIMSYNKNILDIYKKMDSDSA-----ALQLEQIDP 128
D++ IL + ++ N + K D I YNK L + + + +L I
Sbjct: 700 DVQPGEILSQEKEELVNRGYAKCDEKIEEYNKGKLQLQPGCNEEETLEAEILSELSTIRE 759
Query: 129 DISSHILMRLSPRQSSLIMSKMNPKSATM-ITNVVA 163
+ + L PR S LIM+ K + + I+ +VA
Sbjct: 760 EAGKICIRELHPRNSPLIMALCGSKGSKINISQMVA 795
>gnl|CDD|146204 pfam03448, MgtE_N, MgtE intracellular N domain. This domain is
found at the N-terminus of eubacterial magnesium
transporters of the MgtE family pfam01769. This domain
is an intracellular domain that has an alpha-helical
structure. The crystal structure of the MgtE transporter
shows two of 5 magnesium ions are in the interface
between the N domain and the CBS domains. In the absence
of magnesium there is a large shift between the N and
CBS domains.
Length = 102
Score = 26.7 bits (60), Expect = 3.7
Identities = 6/54 (11%), Positives = 23/54 (42%)
Query: 107 ILDIYKKMDSDSAALQLEQIDPDISSHILMRLSPRQSSLIMSKMNPKSATMITN 160
I ++ +++ + L + P+ ++ +L L + ++ + P+ +
Sbjct: 6 IAELLEELPPEERLALLRLLPPERAAEVLEELDEDVQAELLEALPPEELAELLE 59
>gnl|CDD|34518 COG4909, PduC, Propanediol dehydratase, large subunit [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 554
Score = 26.2 bits (57), Expect = 4.9
Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 13/84 (15%)
Query: 93 FQKYDSFIMSYNKNILDIYKKMDSDSAALQLEQIDPDISSHILMRL----SPRQSSLIMS 148
F D FI Y ++ + M DS L DP++ ++RL +P + ++S
Sbjct: 59 FDLIDHFIARYGIDLERAEEVMAMDSVKLANMLCDPNVPRETIVRLTTAMTPAKIVEVVS 118
Query: 149 KMNPKSATMITNVVANMLKFKKLK 172
+M NVV M+ +K++
Sbjct: 119 QM---------NVVEMMMAMQKMR 133
>gnl|CDD|32420 COG2239, MgtE, Mg/Co/Ni transporter MgtE (contains CBS domain)
[Inorganic ion transport and metabolism].
Length = 451
Score = 26.0 bits (57), Expect = 5.2
Identities = 20/119 (16%), Positives = 48/119 (40%), Gaps = 15/119 (12%)
Query: 50 TNVIDSVRERDYLSQKKVLEDLQK----------DIEQRVILLENHKKEYNLWFQKYDSF 99
N+ID + ++D +K+L L +RV++ KE +
Sbjct: 10 ENLIDLLEDKDLSVLRKLLARLHPADVAEILEELPGRERVVVWRLLPKE-----DAAEVL 64
Query: 100 IMSYNKNILDIYKKMDSDSAALQLEQIDPDISSHILMRLSPRQSSLIMSKMNPKSATMI 158
++ +I + + + A +E++D D ++ +L L ++S ++P+ +
Sbjct: 65 GELDDEVREEIIEALSDEELAAAIEELDIDDAADLLDELPDEVRDELLSLLDPEERARV 123
>gnl|CDD|145440 pfam02286, Dehydratase_LU, Dehydratase large subunit. This family
contains the large subunit of the trimeric diol
dehydratases and glycerol dehydratases. These enzymes
are produced by some enterobacteria in response to
growth substances.
Length = 554
Score = 26.2 bits (58), Expect = 5.4
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 4/69 (5%)
Query: 93 FQKYDSFIMSYNKNILDIYKKMDSDSAALQLEQIDPDISSHILMRL----SPRQSSLIMS 148
F D FI Y ++ + M DS L +DP++ ++RL +P + + ++S
Sbjct: 59 FDLIDRFIARYGIDLERAEEAMAMDSVKLARMLVDPNVPREEIVRLTTGMTPAKLAEVVS 118
Query: 149 KMNPKSATM 157
++N M
Sbjct: 119 QLNVVEMMM 127
>gnl|CDD|58174 cd03508, Delta4-sphingolipid-FADS-like, The Delta4-sphingolipid
Fatty Acid Desaturase (Delta4-sphingolipid-FADS)-like
CD includes the integral-membrane enzymes,
dihydroceramide Delta-4 desaturase, involved in the
synthesis of sphingosine; and the human membrane fatty
acid (lipid) desaturase (MLD), reported to modulate
biosynthesis of the epidermal growth factor receptor;
and other related proteins. These proteins are found in
various eukaryotes including vertebrates, higher
plants, and fungi. Studies show that MLD is localized
to the endoplasmic reticulum. As with other members of
this superfamily, this domain family has extensive
hydrophobic regions that would be capable of spanning
the membrane bilayer at least twice. Comparison of
sequences also reveals the existence of three regions
of conserved histidine cluster motifs that contain
eight histidine residues: HXXXH, HXXHH, and HXXHH.
These histidine residues are reported to be
catalytically essential and proposed to be the ligands
for the iron atoms contained within the homolog,
stearoyl CoA desaturase..
Length = 289
Score = 25.9 bits (57), Expect = 5.9
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 1 MILLPIIYYYKKRDMLSQLLFLLFFFLQGFANQS 34
++LL II Y RD + L+ +F G N S
Sbjct: 25 VVLLQIITAYLLRDSSWWKILLVAYFFGGTINHS 58
>gnl|CDD|37502 KOG2291, KOG2291, KOG2291, Oligosaccharyltransferase, alpha subunit
(ribophorin I) [Posttranslational modification, protein
turnover, chaperones].
Length = 602
Score = 25.7 bits (56), Expect = 7.9
Identities = 23/166 (13%), Positives = 54/166 (32%), Gaps = 20/166 (12%)
Query: 6 IIYYYKKRDMLSQLLFLLFFFLQGFANQSYGDPTLVDREIQQYCTNVIDSVRERDYLSQK 65
+ Y + K ML + L ++ F F Y + + + +
Sbjct: 425 VHYTFSKSSMLQEPLLIIAAFFILFFAVIV------------YVRLDFNISSDPSMSATR 472
Query: 66 KV---LEDLQKDIEQRVILLENHKKEYNLWFQKYDSFIMSYNKNILDIYKKMDSDSAALQ 122
+V L L ++ + ++ + + + + + K + KK +
Sbjct: 473 RVFQILLQLALEVNKCDVMYCSLSEGRFRYKNTENIPTLGGAKKSSPLEKKDLASELVPL 532
Query: 123 LEQIDPDISSHILMRLSPRQSSLIMS-KMNPKSATMITNVVANMLK 167
+ S+ + + + L S K+ PK++ M + V K
Sbjct: 533 PSPLKTSDSTCV----ANKLPELSCSVKLVPKTSVMQKHGVEGNGK 574
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.322 0.136 0.379
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,109,407
Number of extensions: 108462
Number of successful extensions: 363
Number of sequences better than 10.0: 1
Number of HSP's gapped: 359
Number of HSP's successfully gapped: 36
Length of query: 175
Length of database: 6,263,737
Length adjustment: 87
Effective length of query: 88
Effective length of database: 4,383,754
Effective search space: 385770352
Effective search space used: 385770352
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: 54 (24.6 bits)