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= 0117.0012.p (306 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pil... 257 1e-69 gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein... 160 1e-40 gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum ser... 105 3e-24 gi|300310145|ref|YP_003774237.1| general secretion pathway prote... 92 5e-20 >gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pilus retraction ATPase PilT protein [Herbaspirillum seropedicae SmR1] Length = 351 Score = 257 bits (656), Expect = 1e-69, Method: Compositional matrix adjust. Identities = 143/238 (60%), Positives = 178/238 (74%), Gaps = 10/238 (4%) Query: 12 SELALRRQGLVLVTGPTGSGKSTTLAAMIRHINEQRSAHILTIEDPIEFIHTPDKSLVSQ 71 +ELA R GLVLVTGPTG+GKS+TLAAMIRH+NE R+ HILTIEDPIEFIHTP ++L+SQ Sbjct: 116 AELAERAGGLVLVTGPTGAGKSSTLAAMIRHLNETRALHILTIEDPIEFIHTPQRALISQ 175 Query: 72 RAVGTHTRSFANALRSALREDPDVILIGELRDLDTIRLALTAAETGHLVLATLHTSSAAK 131 R +GTHT ALR+ALR DPDV+L+GELRD DTIRLALTAAETGHLVL TLH +SAA+ Sbjct: 176 RELGTHTADLPAALRAALRADPDVLLVGELRDADTIRLALTAAETGHLVLGTLHAASAAR 235 Query: 132 SVDRIVDVFPGDEKEMVRSMLSESLSAVVSQILLKTRAGDDRIAAHEIMLGTPAIRNLIR 191 +V+R++DVFP EKE R+ML+ESL V++Q LL T G R+AAHE+++ TPA+RNLIR Sbjct: 236 TVERMLDVFPAGEKEPARAMLAESLQGVIAQTLLPTADGRARVAAHELLVATPAVRNLIR 295 Query: 192 EGKVAQMVSVMQTSAGGGXWSRSCKPRPAPWRRHADAGSLPGRLAAQG-SDHAGDRPR 248 EG+ AQ++S+MQ A G + A R H GR++AQ H G P+ Sbjct: 296 EGRSAQLLSLMQAGAAQGMQTLEA----ALQRLHQQ-----GRISAQTLRQHLGQEPQ 344 >gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 160 bits (406), Expect = 1e-40, Method: Compositional matrix adjust. Identities = 76/165 (46%), Positives = 117/165 (70%) Query: 19 QGLVLVTGPTGSGKSTTLAAMIRHINEQRSAHILTIEDPIEFIHTPDKSLVSQRAVGTHT 78 +G++LVTGPTG+GK+TT+A+M+ +IN R HI+TIE+PIE+ +S++SQ+ V T T Sbjct: 132 KGIILVTGPTGAGKTTTIASMLDYINASRRGHIITIEEPIEYELQRKQSMISQKEVPTDT 191 Query: 79 RSFANALRSALREDPDVILIGELRDLDTIRLALTAAETGHLVLATLHTSSAAKSVDRIVD 138 SF++ LR ALR+ PDV+++GE+RD DT L A E+GHLVLATLHTSSA +++ +++ Sbjct: 192 ESFSSGLREALRQKPDVLMVGEIRDFDTADTVLHAGESGHLVLATLHTSSAVRAITKLLG 251 Query: 139 VFPGDEKEMVRSMLSESLSAVVSQILLKTRAGDDRIAAHEIMLGT 183 FP +++ + L+ESL V+ Q LL + G+ + A E++ Sbjct: 252 FFPQEQRAQRAATLAESLVGVIFQSLLPSEDGEHHVMASEMVFNN 296 >gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum seropedicae SmR1] Length = 377 Score = 105 bits (263), Expect = 3e-24, Method: Compositional matrix adjust. Identities = 60/125 (48%), Positives = 90/125 (72%), Gaps = 8/125 (6%) Query: 17 RRQGLVLVTGPTGSGKSTTLAAMIRHINEQRSAHILTIEDPIEFIHTPDKSLVS--QRAV 74 R G+VL+TGPTGSGK+ +L A ++ +N +I T EDP+E I+ P + VS +RA Sbjct: 146 RPHGMVLMTGPTGSGKTVSLYACLQRLNRP-GINIATAEDPVE-INLPGINQVSINERA- 202 Query: 75 GTHTRSFANALRSALREDPDVILIGELRDLDTIRLALTAAETGHLVLATLHTSSAAKSVD 134 +FA ALR+ LR+DPDV+++GE+RDLDT +A+ AA+TGHLVL+TLHT+ A ++ Sbjct: 203 ---GLNFAVALRAFLRQDPDVLMVGEIRDLDTADIAIKAAQTGHLVLSTLHTNDAPATLT 259 Query: 135 RIVDV 139 R++++ Sbjct: 260 RLLNM 264 >gi|300310145|ref|YP_003774237.1| general secretion pathway protein E [Herbaspirillum seropedicae SmR1] Length = 541 Score = 92.0 bits (227), Expect = 5e-20, Method: Compositional matrix adjust. Identities = 53/127 (41%), Positives = 81/127 (63%), Gaps = 10/127 (7%) Query: 20 GLVLVTGPTGSGKSTTLAAMI--RHINEQRSAHILTIEDPIEF-----IHTPDKSLVSQR 72 G+ +++GPTGSGKSTTL ++ I + H+LTIEDP+E+ + T + S+ Sbjct: 258 GMNIISGPTGSGKSTTLQRVLTGEIIEAEGKLHVLTIEDPVEYPIDGAVQTAVTNAGSEE 317 Query: 73 AVGTHTRSFANALRSALREDPDVILIGELRDLDTIRLALTAAETGHLVLATLHTSSAAKS 132 +R+FA A+ +A+R DPD I+IGE+RD T + AL A+ TGH V T+H +SA Sbjct: 318 ---ERSRAFAAAISNAMRLDPDTIMIGEVRDRATAQNALRASMTGHQVWTTVHANSALAI 374 Query: 133 VDRIVDV 139 +DR++D+ Sbjct: 375 IDRLLDL 381 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 0.318 0.131 0.380 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: 840,197 Number of extensions: 34044 Number of successful extensions: 305 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 302 Number of HSP's successfully gapped: 4 Length of query: 306 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 221 Effective length of database: 1,217,395 Effective search space: 269044295 Effective search space used: 269044295 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 130 (54.7 bits)