BLASTP 2.2.18 [Mar-02-2008]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 0002.0616.p
         (188 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudourid...   298   1e-82
gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudou...    75   5e-15
gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudourid...    64   7e-12
gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [H...    64   8e-12

>gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516
           pseudouridylate synthase [Herbaspirillum seropedicae
           SmR1]
          Length = 188

 Score =  298 bits (764), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 137/188 (72%), Positives = 162/188 (86%)

Query: 1   MPLILFNKPYQVMCQFSAQDDRETLADYLDIPDIYPAGRLDADSEGLMLLTDDGELQHAI 60
           MPLIL NKP+QVM QFSA  +R+TLADY+DIP++YPAGRLDADSEGL+LLTDDG+LQHAI
Sbjct: 1   MPLILLNKPFQVMSQFSAHPERQTLADYIDIPNVYPAGRLDADSEGLLLLTDDGKLQHAI 60

Query: 61  SHPKRKQPKVYLVQVEGTPDANSLERLRNPLDLGDFVTRKSEVRHVQEPAWLWPRNPPIR 120
           +HP+RK PK YL QVEG P   +L++LR PLDLGDFVT+ S+ R +QEP W+WPRNPPIR
Sbjct: 61  AHPRRKLPKTYLAQVEGQPSPEALDKLRQPLDLGDFVTQGSQARLIQEPGWMWPRNPPIR 120

Query: 121 ERKNHPTSWLTIQISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFALATDPLLPGEWKTVD 180
           +R+N PTSW+ + ISEGKNRQVRRMTAAVGLPTLRLVRIAIGPF+LAT P++PGEW+ VD
Sbjct: 121 QRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHPVMPGEWREVD 180

Query: 181 PQEFHRDN 188
           P E  R  
Sbjct: 181 PLELERQG 188


>gi|300311054|ref|YP_003775146.1| ribosomal small subunit
           pseudouridine synthase A [Herbaspirillum seropedicae
           SmR1]
          Length = 240

 Score = 74.7 bits (182), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 54/152 (35%), Positives = 71/152 (46%), Gaps = 17/152 (11%)

Query: 33  DIYPAGRLDADSEGLMLLTDDGELQHAISHPKRKQPKVYLVQVEGTPDANSLERLRNPLD 92
           D+ P GRLD D+ GL+L++DDG   HA S PKR  PKVY            + +L+  + 
Sbjct: 98  DVQPVGRLDHDTTGLLLMSDDGAFIHAQSSPKRHVPKVYAATTAEPVTEALIAQLKAGVQ 157

Query: 93  LGDFVTRKSEVRHVQEPAWLWPRNPPIRERKNHPTSWLTIQISEGKNRQVRRMTAAVGLP 152
           L D            EPA L       R R+    + L I + +GK  QV+RM AA G  
Sbjct: 158 LHD------------EPAPL----AATRCRQL-GENLLEIVLEQGKYHQVKRMLAAAGNH 200

Query: 153 TLRLVRIAIGPFALATDPLLPGEWKTVDPQEF 184
              L R AIG   L    L  GEW  +D ++ 
Sbjct: 201 CSALQRTAIGGLQLEALALEEGEWTYLDAEQM 232


>gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516
           pseudouridylate synthase [Herbaspirillum seropedicae
           SmR1]
          Length = 560

 Score = 63.9 bits (154), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 48/183 (26%), Positives = 83/183 (45%), Gaps = 23/183 (12%)

Query: 3   LILFNKPYQVMCQFSAQDDRETLADYLDIPDIYPA-----GRLDADSEGLMLLTDDGELQ 57
           +++++KP   +   +  + R ++ D L  P +        GRLD ++EGL+L T  G+L 
Sbjct: 260 VLVYHKPAGEIVSHADPEGRNSVFDRL--PTMKAGKWLAVGRLDYNTEGLLLFTTSGDLA 317

Query: 58  HAISHPKRKQPKVYLVQVEGTPDANSLERLRNPLDLGDFVTRKSEVRHVQEPAWLWPRNP 117
           + + HP+    + Y V+  G  +    ++L + ++L D   + S +              
Sbjct: 318 NRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDGPAQFSRIADGGGEGV------ 371

Query: 118 PIRERKNHPTSWLTIQISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFALATDPLLPGEWK 177
                      W  + I EG+NR+VRRM  AVGL   RL+R   G   L    L  G W+
Sbjct: 372 ---------NKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQT-LRRGRWE 421

Query: 178 TVD 180
            ++
Sbjct: 422 ELE 424


>gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase
           [Herbaspirillum seropedicae SmR1]
          Length = 248

 Score = 63.9 bits (154), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 52/170 (30%), Positives = 76/170 (44%), Gaps = 25/170 (14%)

Query: 18  AQDDRETLADYLDIPDIYPAGRLDADSEGLMLLTDDGELQHAISHPKRKQPKVYLVQVE- 76
           A+D  E       +  + PAGRLD DS GL++LT DG +   +        K YLV+V+ 
Sbjct: 98  AEDQTEMRFHPRQLKSLVPAGRLDIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQY 157

Query: 77  ---GTPDANSLERLRNPLDLGDFVTRKSEVRHVQEPAWLWPRNPPIRERKNHPTSWLTIQ 133
              G    + L+RL + L +     R ++V        +W     +R             
Sbjct: 158 TRPGKLPESDLKRLNHGLIMDGKPLRPAKV--------VWQNEDQLR-----------FT 198

Query: 134 ISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFALATDPLLPGEWKTVDPQE 183
           + EGK RQ+RRM   VGL  + L R+ IG   L   P   G+W+ + P E
Sbjct: 199 LREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGELP--TGQWRYLRPDE 246


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.319    0.138    0.426 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 653,401
Number of extensions: 26873
Number of successful extensions: 59
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 56
Number of HSP's successfully gapped: 4
Length of query: 188
Length of database: 1,619,870
Length adjustment: 80
Effective length of query: 108
Effective length of database: 1,241,070
Effective search space: 134035560
Effective search space used: 134035560
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 (21.7 bits)
S2: 128 (53.9 bits)