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= 0001.2339.p (462 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312157|ref|YP_003776249.1| nitrogenase molybdenum-cofactor... 930 0.0 gi|300312159|ref|YP_003776251.1| nitrogenase molybdenum-iron pro... 165 9e-42 >gi|300312157|ref|YP_003776249.1| nitrogenase molybdenum-cofactor synthesis protein NifN protein [Herbaspirillum seropedicae SmR1] Length = 462 Score = 930 bits (2403), Expect = 0.0, Method: Compositional matrix adjust. Identities = 453/462 (98%), Positives = 459/462 (99%) Query: 1 MAIVETSSKAAAVNPLKMSQPLGAAYAFLGMNRCMPVMHGSQGCTSFGLVLLVRHFREAI 60 MAI+ETSSKAAAVNPLKMSQPLGAAYAFLGMNRCMPVMHGSQGCTSFGLVLLVRHFREAI Sbjct: 1 MAIIETSSKAAAVNPLKMSQPLGAAYAFLGMNRCMPVMHGSQGCTSFGLVLLVRHFREAI 60 Query: 61 PLQTTAMNEVSSILGGMENIEKAVLNIRLRAKPDLIAICSTGLTETKGDDVNAYLKLIRQ 120 PLQTTAMNEVSSILGGMENIEKAVLNIRLRAKPDLIAICSTGLTETKGDDVNAYL+LIRQ Sbjct: 61 PLQTTAMNEVSSILGGMENIEKAVLNIRLRAKPDLIAICSTGLTETKGDDVNAYLRLIRQ 120 Query: 121 KHPDLADTALAYVSTPDYTGAFQDGWAKAVEALIRALGEPQPGIQTRAKQVNLLAGCHLT 180 KHPDLADTALAYVSTPDYTGAFQDGWAKAVEALIRALGEPQPG+QTRAKQ+NLLAGCHLT Sbjct: 121 KHPDLADTALAYVSTPDYTGAFQDGWAKAVEALIRALGEPQPGLQTRAKQINLLAGCHLT 180 Query: 181 PADIEELRDIVQSFGLEPIVLPDVSGSLDGHLPDNFSPTSMGGTTLADMRALGASIVTIA 240 PADIEELRDIVQSFGLEPIVLPDVS SLDGHLPDNFSPTSMGGTTLA+MRALGASIV+IA Sbjct: 181 PADIEELRDIVQSFGLEPIVLPDVSSSLDGHLPDNFSPTSMGGTTLAEMRALGASIVSIA 240 Query: 241 IGEQMRASAQAVQELGGVPYVVFDRLTGLQANDRFLAYLEYVSGQPIPARYRRQRSQLQD 300 IGEQMRASAQAVQEL GVPYVVFDRLTGLQANDRFLAYLEYVSGQPIPARYRRQRSQLQD Sbjct: 241 IGEQMRASAQAVQELSGVPYVVFDRLTGLQANDRFLAYLEYVSGQPIPARYRRQRSQLQD 300 Query: 301 AMLDGHFFFGGVKVAIGAEPDLLLSLSAWLAEMGCEIGCAVTTTTSPVLDGVPAARVVIG 360 AMLDGHFFFGGVKVAIGAEPDLLLSLSAWLAEMGCEIGCAVTTTTSPVLDGVPAARVVIG Sbjct: 301 AMLDGHFFFGGVKVAIGAEPDLLLSLSAWLAEMGCEIGCAVTTTTSPVLDGVPAARVVIG 360 Query: 361 DLEDLEQGARRASAGLLVTHSHGRQAAERLHIPFHRAGLPMFDRLGAGHCLSVGYRGTRG 420 DLEDLEQGARRASAGLLVTHSHGRQAAERLHIPFHRAGLPMFDRLGAGHCLSVGYRGTRG Sbjct: 361 DLEDLEQGARRASAGLLVTHSHGRQAAERLHIPFHRAGLPMFDRLGAGHCLSVGYRGTRG 420 Query: 421 LIFEIGNLLLAAGHAHTPDDWQLPQSTRDALALATSVQGESS 462 LIFEIGNLLLAAGHAHTPDDWQLPQSTRDALALAT VQGESS Sbjct: 421 LIFEIGNLLLAAGHAHTPDDWQLPQSTRDALALATPVQGESS 462 >gi|300312159|ref|YP_003776251.1| nitrogenase molybdenum-iron protein beta chain protein [Herbaspirillum seropedicae SmR1] Length = 519 Score = 165 bits (417), Expect = 9e-42, Method: Compositional matrix adjust. Identities = 114/449 (25%), Positives = 207/449 (46%), Gaps = 19/449 (4%) Query: 7 SSKAAAVNPLKMSQPLGAAYAFLGMNRCMPVMHGSQGCTSFGLVLLVRHFREAIPLQTTA 66 + +A +NP K QPLGA YA +G +P +HGSQGC ++ RHF+E +++ Sbjct: 58 AREALTINPAKACQPLGAVYAAVGFQNTLPFVHGSQGCVAYYRSHFSRHFKEPTSCVSSS 117 Query: 67 MNEVSSILGGMENIEKAVLNIRLRAKPDLIAICSTGLTETKGDDVNAYLKLIRQKHPDLA 126 M E +++ GG+ N+ + N KP++IA+ +T + E GDD+++++K + K A Sbjct: 118 MTEDAAVFGGLNNMIDGLANALSLYKPEMIAVSTTCMAEVIGDDLDSFIKNAKDKGSVPA 177 Query: 127 DTALAYVSTPDYTGAFQDGWAKAVEALIRALGEPQ----PGIQTRAKQ-VNLLAGCH-LT 180 + + + TP + G+ G+ A++ ++ + + P ++ + + +N + G Sbjct: 178 EYDVPFAHTPAFVGSHVTGYDNALKGILTHFWDGKAGTVPALERKPNERINFIGGFDGFV 237 Query: 181 PADIEELRDIVQSFGLEPIVLPDVSGSLDGHLPDNFSPTSMGGTTLADMRALGASIVTIA 240 ++ E++ I + G++ ++ D S + F S G T + AL A + Sbjct: 238 VGNLPEVKRIFKLMGVDGTIVCDPSEVWNTPTDGQFRMYSGGTTKQEVIEALDAKATVVF 297 Query: 241 IGEQMRASAQAVQELGGVPYVVFDRLTGLQANDRFLAYLEYVSGQPIPARYRRQRSQLQD 300 +A+ + E G V + G+ D+FL L +SGQPIPA +R +L D Sbjct: 298 QEFSTLKTAKYIAE-KGQEVVTLNHPMGVAGTDQFLMELSRLSGQPIPAELELERGRLVD 356 Query: 301 AMLDGHFFFGGVKVAIGAEPDLLLSLSAWLAEMGCEIGCAVTTT--------TSPVLDGV 352 A+ D G K A+ +PD+++ ++ +L E+GCE ++T +LD Sbjct: 357 AIADSQAHLHGKKFALYGDPDMMIGMTQFLLELGCEPTHILSTNGDAEWAAKVQALLDAS 416 Query: 353 PAAR----VVIGDLEDLEQGARRASAGLLVTHSHGRQAAERLHIPFHRAGLPMFDRLGAG 408 P + DL L L+ +++G+ +P R P+FDR Sbjct: 417 PFGKDCKVYPKRDLWHLRSLLFTEPVDFLIGNTYGKYLERDCGVPLIRLVFPVFDRHHYH 476 Query: 409 HCLSVGYRGTRGLIFEIGNLLLAAGHAHT 437 GY G ++ I + A A+T Sbjct: 477 RFPIWGYAGAMRVLVMILDEYFEALDANT 505 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 0.320 0.136 0.400 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: 1,520,986 Number of extensions: 67626 Number of successful extensions: 259 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 258 Number of HSP's successfully gapped: 2 Length of query: 462 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 373 Effective length of database: 1,198,455 Effective search space: 447023715 Effective search space used: 447023715 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 (21.8 bits) S2: 132 (55.5 bits)