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= 0088.0004.p (322 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value RSp0015 [E] COG4177 ABC-type branched-chain amino acid transport... 197 2e-50 STM1137 [R] COG3381 Uncharacterized component of anaerobic dehyd... 192 4e-49 PA1072 [E] COG4177 ABC-type branched-chain amino acid transport ... 167 2e-41 SMc01950 [E] COG4177 ABC-type branched-chain amino acid transpor... 143 4e-34 BMEI0259 [E] COG4177 ABC-type branched-chain amino acid transpor... 140 2e-33 >RSp0015 [E] COG4177 ABC-type branched-chain amino acid transport system, permease component Length = 299 Score = 197 bits (501), Expect = 2e-50, Method: Compositional matrix adjust. Identities = 116/293 (39%), Positives = 179/293 (61%), Gaps = 5/293 (1%) Query: 31 FSDVTRSMLLLIGVNIMLAVSLNLITGITGQFSIGHAGFMSVGAYTSAILTLDYNVPFIP 90 F V +++L +G+N +LA+S+ L T G ++ +A FM +GAYTSA+LT++ +PF Sbjct: 7 FWSVYSNLVLTLGINALLALSIYL-TLSCGLLAMANAAFMGIGAYTSALLTMNAEMPFPV 65 Query: 91 AILAGGVLAAVFGVLIGMPTLRLNGDYLAIATLGFGEIIRIIMLNTE-YVGGASGLSGIP 149 A+L G + AV V+IG PTLRL+G YLA+ATLGFGE++R+++LNTE + GGA GL+GIP Sbjct: 66 ALLGGMLAPAVVAVIIGRPTLRLSGVYLAMATLGFGEVVRVLILNTESWTGGALGLNGIP 125 Query: 150 AKTTWTMLFLFTLITVVVINNFIGSTHGRXXXXXXXXXXXXXXMGINTTRYKIIAFTIGA 209 T W + L +T+ V+ S GR MGIN K++AF +GA Sbjct: 126 QLTEWWHVALAVALTLFVLARLRRSKVGRAFEAIKEDETAAGLMGINVAGTKLLAFVLGA 185 Query: 210 LFAGMAGGLSAHTFYVITPGSFNFLKSFEIIVMVVLGGLGSTAGSIVGAVFVTLLYTYLR 269 + AG+AG L+AH + I P F F + EI+ M +LGG G ++G+V ++LL LR Sbjct: 186 MIAGLAGALNAHLTFFIGPAEFGFDRGVEILTMAILGGTNGLTGPVLGSVILSLLPELLR 245 Query: 270 EFPEWRMIIYSIVLILMMIFRPSGLLGKTKFSLG---KLGKKEAKANDAISES 319 F ++R+++ ++L+L+++F P G+ +F+ K G A+ A +ES Sbjct: 246 AFKDFRLVVNGLILMLIVLFLPKGIWDPARFARWFGMKRGGTMPGASAASNES 298 >STM1137 [R] COG3381 Uncharacterized component of anaerobic dehydrogenases Length = 289 Score = 192 bits (489), Expect = 4e-49, Method: Compositional matrix adjust. Identities = 0/303 (0%), Positives = 0/303 (0%), Gaps = 36/303 (11%) Query: 41 LIGVNIMLAVSLNLITGITGQFSIGHAGFMSVGAYTSAILTL------------------ 82 + G I + ++ + + + Sbjct: 45 VTGHAIGAYIRARRLSKSAVALRLTARPILDIALQYRFDSQQTFTRAFKKQFAQTPALYR 104 Query: 83 -DYNVPFIPAILAGGVLAAVFGVLIGMPTLRLNGDYLAIATLGFGEIIRIIMLNT-EYVG 140 + + + + E I Sbjct: 105 RSPEWSAFGIRPPLRLGEFTMPEHKFVTLEDTPLIGVTQSYSCSLEQISDFRHEMRYQFW 164 Query: 141 GASGLSGIPAKTTWTMLFLFTLITVVVINNFIGSTHGRXXXXXXXXXXXXXXMGINTTRY 200 + L + T + + Y Sbjct: 165 HDFLGNAPTIPPVLYGLNETRPSQDKDDEQEVFYTTALAQDQADGYVLTGHPVMLQGGEY 224 Query: 201 KIIAFTIGALFAGMAGGLSAHTFYVITPGSFNF--LKSFEIIVMVVLGGLGSTAGSIVGA 258 + + T + + G Sbjct: 225 VMFTYEGLGTGVQEFILTVYGTCMPMLNLTRRKGQDIERYYPAEDAKAGDRPINLRCELL 284 Query: 259 VFVTLLYTYLREFPE--------------WRMIIYSIVLILMMIFRPSGLLGKTKFSLGK 304 Sbjct: 285 344 Query: 305 LGK 307 Sbjct: 345 347 >PA1072 [E] COG4177 ABC-type branched-chain amino acid transport system, permease component Length = 417 Score = 167 bits (423), Expect = 2e-41, Method: Compositional matrix adjust. Identities = 116/296 (39%), Positives = 161/296 (54%), Gaps = 35/296 (11%) Query: 41 LIGVNIMLAVSLNLITGITGQFSIGHAGFMSVGAYTSAILTLDYNVPFIPAILAGGVLAA 100 LI + +ML + LN++ G+ G +G+ GF +VGAYT A+L F A+ G++AA Sbjct: 119 LILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAA 178 Query: 101 VFGVLIGMPTLRLNGDYLAIATLGFGEIIRIIMLN-TEYVGGASGLSGIPAKTTWTMLF- 158 +FG L+G P LRL GDYLAI TLGFGEIIRI++ N TE GG +G+ IP T + + F Sbjct: 179 LFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFE 238 Query: 159 --------------------------------LFTLITVVVINNFIGSTHGRXXXXXXXX 186 L L+ + VIN + GR Sbjct: 239 RRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALRED 298 Query: 187 XXXXXXMGINTTRYKIIAFTIGALFAGMAGGLSAHTFYVITPGSFNFLKSFEIIVMVVLG 246 +G+N T K+ AFTIGA FAG AG A ++TP SF F++S I+ +VVLG Sbjct: 299 EVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLG 358 Query: 247 GLGSTAGSIVGAVFVTLLYTYLREFPEWRMIIYSIVLILMMIFRPSGLLGKTKFSL 302 G+GS G I+ AV + LL +R F E+RM+I+ + +I+MMI+RP GLL + L Sbjct: 359 GMGSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHL 413 >SMc01950 [E] COG4177 ABC-type branched-chain amino acid transport system, permease component Length = 461 Score = 143 bits (360), Expect = 4e-34, Method: Compositional matrix adjust. Identities = 102/299 (34%), Positives = 152/299 (50%), Gaps = 43/299 (14%) Query: 44 VNIMLAVSLNLITGITGQFSIGHAGFMSVGAYTSAILTLDYNVPFIPAILAGGVLAAVFG 103 + +MLA LN++ G+ G +G+ F +VGAY+ A+L+ + + F + G+LAA +G Sbjct: 142 IYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPIAGLLAACWG 201 Query: 104 VLIGMPTLRLNGDYLAIATLGFGEIIRIIMLN-TEYVGGASGLSGI-------------- 148 V++G P LRL GDYLAI TL FGEIIR++++N TE G G+SGI Sbjct: 202 VVLGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTEVTKGTFGVSGIAKATLFGIKFDATK 261 Query: 149 ---------PAKTTWTMLFLFTLI------TVVVINNFIGSTHGRXXXXXXXXXXXXXXM 193 P + + +FLF LI T V GR + Sbjct: 262 DGFAAMMGLPMSSAYYKIFLFYLILGLALLTAFVTIRLRRMPIGRAWEALREDEIACRSL 321 Query: 194 GINTTRYKIIAFTIGALFAGMAGGLSAHTFYVITPGSFNFLKSFEIIVMVVLGGLGSTAG 253 GINT K+ AF GA+F G AG A ++P SF FL+S I+ +VVLGG+GS G Sbjct: 322 GINTVTTKLTAFATGAMFGGFAGSFFAVRQGFVSPESFVFLESAVILAIVVLGGMGSLTG 381 Query: 254 SIVGAVFVTLLYTYLREF------------PE-WRMIIYSIVLILMMIFRPSGLLGKTK 299 + AV + LRE PE +RM+I+ + ++++M+++P G +G + Sbjct: 382 IAIAAVVMIGGTEILRELTFLKMIFGPTFTPELYRMLIFGLAMVVVMVWKPRGFVGSRE 440 >BMEI0259 [E] COG4177 ABC-type branched-chain amino acid transport system, permease component Length = 459 Score = 140 bits (354), Expect = 2e-33, Method: Compositional matrix adjust. Identities = 100/301 (33%), Positives = 152/301 (50%), Gaps = 43/301 (14%) Query: 44 VNIMLAVSLNLITGITGQFSIGHAGFMSVGAYTSAILTLDYNVPFIPAILAGGVLAAVFG 103 + +MLA LN++ G+ G +G+ F +VGAY+ AIL+ + + F + G+LAA +G Sbjct: 140 IYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYAILSSYFGLSFWVLLPIAGLLAATWG 199 Query: 104 VLIGMPTLRLNGDYLAIATLGFGEIIRIIMLN-TEYVGGASGLSGIPAKTTWTMLF---- 158 +++G P LRL GDYLAI TL FGEIIR++++N T+ G G+SGI T + + F Sbjct: 200 IILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDLTRGTFGISGIAKATFFGLPFNASK 259 Query: 159 -------------------------LFTLITVVVINNFIGSTHGRXXXXXXXXXXXXXXM 193 L L+T V GR + Sbjct: 260 DGFAAHFGLAFSAAHYKFFLYYVILLLALLTAWVTIRLRRMPVGRAWEALREDEIACRSL 319 Query: 194 GINTTRYKIIAFTIGALFAGMAGGLSAHTFYVITPGSFNFLKSFEIIVMVVLGGLGSTAG 253 GINTT K+ AF GA+F G AG A ++P SF FL+S I+ +VVLGG+GS G Sbjct: 320 GINTTTTKLTAFATGAMFGGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLVG 379 Query: 254 SIVGAVFVTLLYTYLREF------------PE-WRMIIYSIVLILMMIFRPSGLLGKTKF 300 + A+ + LRE PE +RM+I+ + ++++M+++P G +G + Sbjct: 380 IAIAAIVMIGGTEILREMSFLKIIFGPDFTPELYRMLIFGLAMVVVMVWKPRGFVGSREP 439 Query: 301 S 301 S Sbjct: 440 S 440 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 Lambda K H 0.327 0.143 0.415 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 115334 Number of Hits to DB: 21,607,895 Number of extensions: 868665 Number of successful extensions: 4279 Number of sequences better than 1.0e-05: 90 Number of HSP's gapped: 4202 Number of HSP's successfully gapped: 94 Length of query: 322 Length of database: 38,378,431 Length adjustment: 106 Effective length of query: 216 Effective length of database: 26,153,027 Effective search space: 5649053832 Effective search space used: 5649053832 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 116 (49.3 bits)