GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Pseudomonas stutzeri RCH2

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate GFF1023 Psest_1056 2-isopropylmalate synthase, bacterial type

Query= BRENDA::Q9JZG1
         (517 letters)



>FitnessBrowser__psRCH2:GFF1023
          Length = 514

 Score =  667 bits (1722), Expect = 0.0
 Identities = 340/514 (66%), Positives = 415/514 (80%), Gaps = 2/514 (0%)

Query: 1   MTQTNRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAV 60
           M+  +RVIIFDTTLRDGEQSPGA+MT EEK+R+AR LE+L VD+IEAGFA ASPGDF AV
Sbjct: 1   MSSNDRVIIFDTTLRDGEQSPGASMTAEEKLRIARALERLKVDVIEAGFAIASPGDFAAV 60

Query: 61  NAIAKTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQV 120
             +A  I  STVCSL+RA++ DI +A EA+A A   RIHTFIATSPIHM+YKL+M+P QV
Sbjct: 61  KLVADNIKDSTVCSLARAVDADIERAAEALAGANSGRIHTFIATSPIHMQYKLRMQPDQV 120

Query: 121 IEAAVKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPY 180
           +E AV+AVK AR    DVEFSCEDA RSEIDFL  I  A I+AGA TINIPDTVGY+IP+
Sbjct: 121 VEQAVRAVKKARSLCADVEFSCEDAGRSEIDFLCRIIKAAIDAGARTINIPDTVGYAIPH 180

Query: 181 KTEEFFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGN 240
           +  +  R+L+ + PN  K V+S HCHNDLGLAVANSLAA+  GARQVECT+NGLGERAGN
Sbjct: 181 QYADTIRQLLERIPNADKAVFSVHCHNDLGLAVANSLAAVVAGARQVECTINGLGERAGN 240

Query: 241 ASVEEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESG 300
           A++EEIVMA+K R DL  + T I+T  I+ +S+LVS ITG+PVQPNKAIVGANAF+HESG
Sbjct: 241 AALEEIVMAIKTRQDLINVHTRIETEHILAASRLVSGITGFPVQPNKAIVGANAFAHESG 300

Query: 301 IHQDGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAF 360
           IHQDGVLKHRETYEIMSA+SVGW  N++ +GK SGR AF+++L +LGI LE +E LNAAF
Sbjct: 301 IHQDGVLKHRETYEIMSAQSVGWNANKMVMGKHSGRAAFRSRLDELGIVLEGDE-LNAAF 359

Query: 361 ARFKELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIKGE 420
           ARFKELADKK EIFDEDL ALVSD +     E +K  S +++++TG  P A +V S+ G 
Sbjct: 360 ARFKELADKKHEIFDEDLQALVSDTLADEAPEHFKLASLEVASKTGTIPEAKLVISVDGA 419

Query: 421 EKRASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNG 480
           E+ A A GSGPVDA FKAIE+VA+SGA LQ+YSVNA+TQGT+SQGE +VRL +G R+VNG
Sbjct: 420 ERSAQAQGSGPVDATFKAIEAVAESGATLQLYSVNAITQGTDSQGEVTVRLEKGGRIVNG 479

Query: 481 QGADTDVLVATAKAYLSALSKLEFSA-AKPKAQG 513
            GADTD++VA+AKAYL+AL+ ++  A A P+ +G
Sbjct: 480 NGADTDIVVASAKAYLNALNLMQVGAKAHPQVEG 513


Lambda     K      H
   0.313    0.129    0.352 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 700
Number of extensions: 22
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 517
Length of database: 514
Length adjustment: 35
Effective length of query: 482
Effective length of database: 479
Effective search space:   230878
Effective search space used:   230878
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: 52 (24.6 bits)

Align candidate GFF1023 Psest_1056 (2-isopropylmalate synthase, bacterial type)
to HMM TIGR00973 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))

Software error:

../bin/blast/fastacmd -i /tmp/list.8427.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8427.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.