RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 029752
(188 letters)
>gnl|CDD|233294 TIGR01159, DRP1, density-regulated protein DRP1. This protein
family shows weak but suggestive similarity to
translation initiation factor SUI1 and its prokaryotic
homologs.
Length = 173
Score = 204 bits (521), Expect = 6e-68
Identities = 78/176 (44%), Positives = 102/176 (57%), Gaps = 6/176 (3%)
Query: 7 PVRVLYCAVCSLPAEYCEFGPDLEKCKPWLIQNTPDLYPDLAEELNSR---EADKVGEQL 63
P+RVLYC VCSLP EYCEF DL++CK WL +N PDLY L + EA +GE
Sbjct: 1 PLRVLYCGVCSLPPEYCEFSGDLKRCKVWLSENAPDLYAKLYGTDSPTAEAEAVTIGEAQ 60
Query: 64 QSTGISSPASSAPKAEEVKHLPGGKIKKKDKKEVVIEKVVRNKRKCITTVKGLELFGVKL 123
+ G E GGK KKK ++V I++ R KRK +T +KGLE F + L
Sbjct: 61 EEKGEKDLLGIQKAQEAR---EGGKKKKKLPQKVTIKREPRTKRKFVTVIKGLETFDIDL 117
Query: 124 SDASKKLGKKFATGASVVKGPTEKEQIDVQGDISYDIVEFITDTWPDVPETAIFFI 179
ASK +KFATG SV K T KE+I +QGD+ DI ++I + WP+V + I +
Sbjct: 118 KKASKTFAQKFATGCSVSKSVTGKEEIVIQGDVMDDIEDYIHEKWPEVGDKDIKDL 173
>gnl|CDD|211320 cd11607, DENR_C, C-terminal domain of DENR and related proteins.
DENR (density regulated protein), together with MCT-1
(multiple copies T cell malignancies), has been shown to
have similar function as eIF2D translation initiation
factor (also known as ligatin), which is involved in the
recruitment and delivery of aminoacyl-tRNAs to the
P-site of the eukaryotic ribosome in a GTP-independent
manner.
Length = 86
Score = 131 bits (331), Expect = 4e-40
Identities = 41/86 (47%), Positives = 58/86 (67%)
Query: 95 KEVVIEKVVRNKRKCITTVKGLELFGVKLSDASKKLGKKFATGASVVKGPTEKEQIDVQG 154
+V I+++ RNKRK +TTV GLE FG+ L A+K KKFA GASV KG K++I +QG
Sbjct: 1 SKVTIKRISRNKRKFVTTVTGLETFGIDLKKAAKLFAKKFACGASVTKGAEGKDEIVIQG 60
Query: 155 DISYDIVEFITDTWPDVPETAIFFIE 180
D++ DIV+ I + WP++ E I +
Sbjct: 61 DVTDDIVDLILEKWPEIDEDNIEILG 86
>gnl|CDD|216391 pfam01253, SUI1, Translation initiation factor SUI1.
Length = 74
Score = 72.1 bits (178), Expect = 3e-17
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 4/78 (5%)
Query: 91 KKDKKEVVIEKVVRNKRKCITTVKGLELFGVKLSDASKKLGKKFATGASVVKGPTEKEQI 150
KK+ +++ I + R K +T V GLELFG+ L +K+L KKF G +V G E+I
Sbjct: 1 KKEDQKIRIRREKRRGGKTVTVVTGLELFGIDLKKLAKELKKKFGCGGTVKDG----EEI 56
Query: 151 DVQGDISYDIVEFITDTW 168
++QGD + + +
Sbjct: 57 EIQGDHRDKVKDLLEKEG 74
>gnl|CDD|223102 COG0023, SUI1, Translation initiation factor 1 (eIF-1/SUI1) and
related proteins [Translation, ribosomal structure and
biogenesis].
Length = 104
Score = 58.9 bits (143), Expect = 7e-12
Identities = 26/91 (28%), Positives = 45/91 (49%), Gaps = 5/91 (5%)
Query: 76 PKAEEVKHLPGGKIKKKDKKEVVIEKVVRNKRKCITTVKGLELFGVKLSDASKKLGKKFA 135
+ K L ++ K+ + V I + R K K +T ++GL+L + L +K+L KK A
Sbjct: 8 GRIGLPKELTCEEVAKEGDQIVRIRRETRRKGKTVTIIEGLDLKDIDLKKLAKELKKKCA 67
Query: 136 TGASVVKGPTEKEQIDVQGDISYDIVEFITD 166
G +V G +I++QGD + E +
Sbjct: 68 CGGTVKDG-----EIEIQGDHRDKVKELLIK 93
>gnl|CDD|211321 cd11608, eIF2D_C, C-terminal domain of eIF2D and related proteins.
eIF2D translation initiation factor (also known as
ligatin) is involved in the recruitment and delivery of
aminoacyl-tRNAs to the P-site of the eukaryotic ribosome
in a GTP-independent manner.
Length = 85
Score = 48.3 bits (116), Expect = 4e-08
Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 4/75 (5%)
Query: 96 EVVIEKVVRNKRKCITTVKGLELFGVKLSDASKKLGKKFATGASVVKGPTEKE--QIDVQ 153
++ E+ NK+ +T + GLE FG+ + +K+L KK A SV P +K+ ++ VQ
Sbjct: 3 DITTERRQGNKK--VTLISGLESFGIDPEEFAKELQKKCAASTSVSPLPGKKKGVEVQVQ 60
Query: 154 GDISYDIVEFITDTW 168
G+ + + +T+ +
Sbjct: 61 GNQVKFVAKLLTEKY 75
>gnl|CDD|211318 cd11566, eIF1_SUI1, Eukaryotic initiation factor 1. eIF1/SUI1
(eukaryotic initiation factor 1) plays an important role
in accurate initiator codon recognition during
translation initiation. eIF1 interacts with 18S rRNA in
the 40S ribosomal subunit during eukaryotic translation
initiation. Point mutations in the yeast eIF1 implicate
the protein in maintaining accurate start-site selection
but its mechanism of action is unknown.
Length = 84
Score = 44.8 bits (107), Expect = 7e-07
Identities = 27/64 (42%), Positives = 37/64 (57%), Gaps = 3/64 (4%)
Query: 104 RNKRKCITTVKGL-ELFGVKLSDASKKLGKKFATGASVVKGPTEKEQIDVQGDISYDIVE 162
RN RK +TTV+GL E F +K K K+FA +VV+ P E I +QGD +I E
Sbjct: 10 RNGRKTLTTVQGLPEEFDLKK--ILKAFKKEFACNGTVVEDPEYGEVIQLQGDQRKNIKE 67
Query: 163 FITD 166
F+ +
Sbjct: 68 FLLE 71
>gnl|CDD|211317 cd00474, eIF1_SUI1_like, Eukaryotic initiation factor 1 and related
proteins. Members of the eIF1/SUI1 (eukaryotic
initiation factor 1) family are found in eukaryotes,
archaea, and some bacteria; eukaryotic members are
understood to play an important role in accurate
initiator codon recognition during translation
initiation. eIF1 interacts with 18S rRNA in the 40S
ribosomal subunit during eukaryotic translation
initiation. Point mutations in the yeast eIF1 implicate
the protein in maintaining accurate start-site selection
but its mechanism of action is unknown. The function of
non-eukaryotic family members is also unclear.
Length = 78
Score = 40.5 bits (95), Expect = 3e-05
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 97 VVIEKVVRNKRKCITTVKGLELFGVKLSDASKKLGKKFATGASVVKGPTEKEQIDVQGDI 156
+ I+ R+ K +T V+GL + + L + +L KK G SV EK +I++QGD
Sbjct: 2 IHIKVEQRSGGKKVTKVEGLPAY-IDLRKLADELKKKLGCGGSVEG---EKMEIEIQGDH 57
Query: 157 SYDIVEFITDTWPDV 171
+ I+ + + D
Sbjct: 58 TDQIIVALEEKGIDK 72
>gnl|CDD|130228 TIGR01160, SUI1_MOF2, translation initiation factor SUI1,
eukaryotic. Alternate name: MOF2. A similar protein
family (see TIGRFAMs model TIGR01158) is found in
prokaryotes. The human proteins complements a yeast SUI1
mutatation [Protein synthesis, Translation factors].
Length = 110
Score = 40.2 bits (94), Expect = 8e-05
Identities = 24/61 (39%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 104 RNKRKCITTVKGLELFGVKLSDASKKLGKKFATGASVVKGPTEKEQIDVQGDISYDIVEF 163
RN RK +TTV+GL L K L K+FA +V++ P E I +QGD ++ EF
Sbjct: 35 RNGRKTLTTVQGLPK-EYDLKKIVKALKKEFACNGTVIEDPEMGEVIQLQGDQRKNVCEF 93
Query: 164 I 164
+
Sbjct: 94 L 94
>gnl|CDD|179173 PRK00939, PRK00939, translation initiation factor Sui1; Reviewed.
Length = 99
Score = 33.7 bits (78), Expect = 0.011
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 8/64 (12%)
Query: 95 KEVVIEKVVRNKR---KCITTVKGLELFGVKLSDASKKLGKKFATGASVVKGPTEKEQID 151
KE K+ +KR K +T ++G++ + L + +KKL K A G +V G +I+
Sbjct: 21 KEQQRIKIKVDKRRYGKEVTIIEGIDPKDIDLKELAKKLKSKLACGGTVKDG-----RIE 75
Query: 152 VQGD 155
+QGD
Sbjct: 76 LQGD 79
>gnl|CDD|130226 TIGR01158, SUI1_rel, translation initation factor SUI1, putative,
prokaryotic. This family of archaeal and bacterial
proteins is homologous to the eukaryotic translation
intiation factor SUI1 involved in directing the ribosome
to the proper start site of translation by functioning
in concert with eIF-2 and the initiator tRNA-Met
[Protein synthesis, Translation factors].
Length = 101
Score = 32.7 bits (75), Expect = 0.030
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 9/68 (13%)
Query: 92 KDKKEVVIEKVVRNKR----KCITTVKGLELFGVKLSDASKKLGKKFATGASVVKGPTEK 147
KE + ++ R R K +T ++GL+L + L + +K+L K G +V G
Sbjct: 18 AKPKEDQVVRIQRETRGRKGKGVTIIEGLDLSDIDLKELAKELKSKCGCGGTVKDG---- 73
Query: 148 EQIDVQGD 155
I++QGD
Sbjct: 74 -VIEIQGD 80
>gnl|CDD|211319 cd11567, YciH_like, Homologs of eIF1/SUI1 including Escherichia
coli YciH. Members of the eIF1/SUI1 (eukaryotic
initiation factor 1) family are found in eukaryotes,
archaea, and some bacteria; eukaryotic members are
understood to play an important role in accurate
initiator codon recognition during translation
initiation. The function of non-eukaryotic family
members is unclear. Escherichia coli YciH is a
non-essential protein and was reported to be able to
perform some of the functions of IF3 in prokaryotic
initiation.
Length = 76
Score = 31.7 bits (73), Expect = 0.039
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 9/70 (12%)
Query: 101 KVVRNKR----KCITTVKGLELFGVKLSDASKKLGKKFATGASVVKGPTEKEQIDVQGDI 156
+V KR K +T ++GL L L + +K+L KK G +V + +I++QGD
Sbjct: 4 RVRLEKRGRGGKTVTVIEGLPLSEEDLKELAKELKKKCGCGGTV-----KDGEIELQGDH 58
Query: 157 SYDIVEFITD 166
I E +
Sbjct: 59 REKIKELLEK 68
>gnl|CDD|168689 PRK06824, PRK06824, translation initiation factor Sui1; Validated.
Length = 118
Score = 29.7 bits (67), Expect = 0.36
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 12/61 (19%)
Query: 102 VVRNKR-------KCITTVKGLELFGVKLSDASKKLGKKFATGASVVKGPTEKEQIDVQG 154
+VR +R K +T + G+ L L + +K+L ++ TG ++ G I++QG
Sbjct: 42 IVRVRRETKGRGGKTVTVITGVPLAEDALKELAKELKRRCGTGGTLKDG-----VIEIQG 96
Query: 155 D 155
D
Sbjct: 97 D 97
>gnl|CDD|214950 smart00978, Tim44, Tim44 is an essential component of the
machinery that mediates the translocation of
nuclear-encoded proteins across the mitochondrial inner
membrane. Tim44 is thought to bind phospholipids of
the mitochondrial inner membrane both by electrostatic
interactions and by penetrating the polar head group
region.
Length = 147
Score = 28.4 bits (64), Expect = 1.3
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 3/29 (10%)
Query: 28 DLEKCKPWLIQNTPDLYPDLAEELNSREA 56
DLE + L TP++Y +LA ++ REA
Sbjct: 38 DLETLRELL---TPEMYNELAAQIAEREA 63
>gnl|CDD|202957 pfam04280, Tim44, Tim44-like domain. Tim44 is an essential
component of the machinery that mediates the
translocation of nuclear-encoded proteins across the
mitochondrial inner membrane. Tim44 is thought to bind
phospholipids of the mitochondrial inner membrane both
by electrostatic interactions and by penetrating the
polar head group region. This family includes the
C-terminal region of Tim44 that has been shown to form
a stable proteolytic fragment in yeast. This region is
also found in a set of smaller bacterial proteins. The
molecular function of the bacterial members of this
family is unknown but transport seems likely. The
crystal structure of the C terminal of Tim44 has
revealed a large hydrophobic pocket which might play an
important role in interacting with the acyl chains of
lipid molecules in the mitochondrial membrane.
Length = 146
Score = 28.4 bits (64), Expect = 1.3
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 28 DLEKCKPWLIQNTPDLYPDLAEELNSREADKVGEQL 63
DLE + L TP++Y + A + REA +
Sbjct: 38 DLETLRELL---TPEVYEEFAAAIAEREAQGLTNDS 70
>gnl|CDD|240341 PTZ00272, PTZ00272, heat shock protein 83 kDa (Hsp83); Provisional.
Length = 701
Score = 28.9 bits (64), Expect = 1.6
Identities = 23/62 (37%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 52 NSREADKVGEQLQSTGISSPASSAPKAEEVKHLPGGKIKKKDK-KEVVIEKVVRNKRKCI 110
+ E + E + T + PK EEVK GK KK K KEV E V+NK K +
Sbjct: 209 KTTEKEVTDEDEEDTKKADEDGEEPKVEEVKEGDEGKKKKTKKVKEVTKEYEVQNKHKPL 268
Query: 111 TT 112
T
Sbjct: 269 WT 270
>gnl|CDD|227418 COG5086, COG5086, Uncharacterized conserved protein [Function
unknown].
Length = 218
Score = 28.0 bits (62), Expect = 2.4
Identities = 20/59 (33%), Positives = 25/59 (42%), Gaps = 7/59 (11%)
Query: 27 PDLEK-CKPWLIQN---TPDLYPDLAEELNSREADKVGEQLQSTGISSPASSAPKAEEV 81
PDL W QN TP L P A L R D++ EQ + I+ S A E +
Sbjct: 22 PDLNDLILAW--QNERSTPRLLP-YALHLIDRFLDRISEQTEHVKIALGKSIAKNNESI 77
>gnl|CDD|163356 TIGR03614, RutB, pyrimidine utilization protein B. RN RM
PMID:16540542 RT A previously undescribed pathway for
pyrimidine catabolism. RA Loh KD, Gyaneshwar P,
Markenscoff Papadimitriou E, Fong R, Kim KS, Parales R,
Zhou Z, Inwood W, Kustu S RL Proc Natl Acad Sci U S A.
2006 Mar 28;103(13):5114-9. Epub 2006 Mar 15.
Length = 226
Score = 27.5 bits (61), Expect = 3.7
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 116 LELFGVKLSDASKKLGKKFATGASV 140
LE FGV L DA+ + G F A++
Sbjct: 175 LEYFGVVLEDATHQAGPDFMQKAAL 199
>gnl|CDD|113413 pfam04642, DUF601, Protein of unknown function, DUF601. This
family represents a conserved region found in several
uncharacterized plant proteins.
Length = 311
Score = 27.7 bits (61), Expect = 3.9
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 54 READKVGEQLQSTGISSPASSAPKAEEVKHLPG---GKIKKKDKKEVVI 99
R ADK +Q + S P SS P+ EE P K KK D +++V+
Sbjct: 61 RYADKKRKQSEKDARSPPRSSRPRTEEKDAGPSQQKEKGKKGDSQDLVV 109
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 27.9 bits (63), Expect = 4.0
Identities = 13/63 (20%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 46 DLAEELNSREADKVGEQLQSTGISSPASSAPKAEEVKHLPGGKIKKKDKKEVVIEKVVRN 105
+LA+EL + ++ E+L+ GI + S+ EE K + +++ + E+
Sbjct: 8 ELAKELG-VSSKELLEKLKELGIEVKSHSSTVEEEEARKEEAKREAEEEAKAEAEEAAAA 66
Query: 106 KRK 108
+ +
Sbjct: 67 EAE 69
>gnl|CDD|193535 cd05659, M18_API, M18 Peptidase Aminopeptidase I. Peptidase M18
family, Aminopeptidase I (Vacuolar aminopeptidase I;
Polypeptidase; Leucine aminopeptidase IV; LAPIV;
Aminopeptidase III; Aminopeptidase yscI; EC 3.4.11.22)
subfamily. Aminopeptidase I is widely distributed in
bacteria and eukaryotes, but only the yeast enzyme has
been characterized to date. It is a vacuolar enzyme,
synthesized as a cytosolic proform, and proteolytically
matured upon arrival in the vacuole. The
pro-aminopeptidase I (proAPI) does not enter the vacuole
via the secretory pathway. In non-starved cells, it uses
the cytoplasm to vacuole targeting (cvt) pathway and in
cells starved for nitrogen, it is targeted to the
vacuole via autophagy. Yeast aminopeptidase I is active
only in its dodecameric form with broad substrate
specificity, acting on all aminoacyl and peptidyl
derivatives that contain a free alpha-amino group; this
is in contrast to the highly selective M18 mammalian
aspartyl aminopeptidase. N-terminal leucine and most
other hydrophobic amino acid residues are the best
substrates while glycine and charged amino acid residues
in P1 position are cleaved much more slowly. This enzyme
is strongly and specifically activated by zinc (Zn2+)
and chloride (Cl-) ions.
Length = 443
Score = 27.9 bits (63), Expect = 4.1
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 41 PDLYPDLAEELNSREADKV--GEQLQSTGISSPASSAPKAEEVK 82
PDL P LA++ ++A + GE+L S P + E+VK
Sbjct: 153 PDLLPHLAKDQMEKKASEAIEGEKLNILVGSIPLKDEKEKEKVK 196
>gnl|CDD|233445 TIGR01511, ATPase-IB1_Cu, copper-(or silver)-translocating P-type
ATPase. This model describes the P-type ATPase
primarily responsible for translocating copper ions
accross biological membranes. These transporters are
found in prokaryotes and eukaryotes. This model
encompasses those species which pump copper ions out of
cells or organelles (efflux pumps such as CopA of
Escherichia coli ) as well as those which pump the ion
into cells or organelles either for the purpose of
supporting life in extremely low-copper environments
(for example CopA of Enterococcus hirae ) or for the
specific delivery of copper to a biological complex for
which it is a necessary component (for example FixI of
Bradyrhizobium japonicum, or CtaA and PacS of
Synechocystis). The substrate specificity of these
transporters may, to a varying degree, include silver
ions (for example, CopA from Archaeoglobus fulgidus).
Copper transporters from this family are well known as
the genes which are mutated in two human disorders of
copper metabolism, Wilson's and Menkes' diseases. The
sequences contributing to the seed of this model are all
experimentally characterized. The copper P-type ATPases
have been characterized as Type IB based on a
phylogenetic analysis which combines the
copper-translocating ATPases with the
cadmium-translocating species. This model and that
describing the cadmium-ATPases (TIGR01512) are well
separated, and thus we further type the copper-ATPases
as IB1 (and the cadmium-ATPases as IB2). Several
sequences which have not been characterized
experimentally fall just below the cutoffs for both of
these models. A sequence from Enterococcus faecalis
scores very high against this model, but yet is
annotated as an "H+/K+ exchanging ATPase". BLAST of this
sequence does not hit anything else annotated in this
way. This error may come from the characterization paper
published in 1987. Accession GP|7415611 from
Saccharomyces cerevisiae appears to be mis-annotated as
a cadmium resistance protein. Accession
OMNI|NTL01HS00542 from Halobacterium which scores above
trusted for this model is annotated as
"molybdenum-binding protein" although no evidence can be
found for this classification [Cellular processes,
Detoxification, Transport and binding proteins, Cations
and iron carrying compounds].
Length = 572
Score = 27.6 bits (62), Expect = 4.1
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 122 KLSDASKKLGKKFATGASVVKGPTEKEQIDVQ----GDI 156
+ SDA KL K + A+++ E E++ V+ GDI
Sbjct: 77 RASDALSKLAKLQPSTATLLTDDGEIEEVPVELLQPGDI 115
>gnl|CDD|235270 PRK04286, PRK04286, hypothetical protein; Provisional.
Length = 298
Score = 27.2 bits (61), Expect = 4.8
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 151 DVQGDISYDIVEFITDTWPDV 171
DVQG ++ + VEFI + PDV
Sbjct: 185 DVQGPLNDEAVEFILEKKPDV 205
>gnl|CDD|148679 pfam07218, RAP1, Rhoptry-associated protein 1 (RAP-1). This family
consists of several rhoptry-associated protein 1 (RAP-1)
sequences which appear to be specific to Plasmodium
falciparum.
Length = 790
Score = 27.3 bits (60), Expect = 6.8
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 87 GKIKKKDKKEVVIEKVVRNKRKCITTVKGLELFGVKLSDASKKLG 131
G+I +KE +I K+ + ++C+ K LF +L+D K G
Sbjct: 372 GEIDDIHEKEAIINKIFDHNKECL---KNFGLFDFELNDNKCKFG 413
>gnl|CDD|187804 cd09673, Cas3_Cas2_I-F, CRISPR/Cas system-associated protein
Cas3/Cas2. CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins comprise
a system for heritable host defense by prokaryotic cells
against phage and other foreign DNA; Cas3/Cas2 fusion;
This protein includes both DEAH and HD motifs for
helicase and N-terminal domain corresponding to Cas2
RNAse; signature gene for Type I and subtype I-F.
Length = 1106
Score = 26.8 bits (59), Expect = 8.5
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 34 PWLIQNTPDLYPDLAEELN 52
PW + +T DLAEELN
Sbjct: 1054 PWWLASTLQQLKDLAEELN 1072
>gnl|CDD|233928 TIGR02562, cas3_yersinia, CRISPR-associated helicase Cas3, subtype
I-F/YPEST. The helicase in many CRISPR-associated (cas)
gene clusters is designated Cas3, and most Cas3 proteins
are described by model TIGR01587. Members of this family
are considerably larger, show a number of motifs in
common with TIGR01587 sequences, and replace Cas3 in some
CRISPR/cas loci in a number of Proteobacteria, including
Yersinia pestis, Chromobacterium violaceum, Erwinia
carotovora subsp. atroseptica SCRI1043, Photorhabdus
luminescens subsp. laumondii TTO1, Legionella
pneumophila, etc [Mobile and extrachromosomal element
functions, Other].
Length = 1110
Score = 26.8 bits (59), Expect = 8.6
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 34 PWLIQNTPDLYPDLAEELN 52
PW + +T DLAEELN
Sbjct: 1058 PWWLASTLQQLKDLAEELN 1076
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 0.389
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,582,049
Number of extensions: 873651
Number of successful extensions: 635
Number of sequences better than 10.0: 1
Number of HSP's gapped: 624
Number of HSP's successfully gapped: 36
Length of query: 188
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 97
Effective length of database: 6,901,388
Effective search space: 669434636
Effective search space used: 669434636
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: 56 (25.4 bits)