GapMind for catabolism of small carbon sources

 

Alignments for a candidate for maiA in Herbaspirillum seropedicae SmR1

Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate HSERO_RS05615 HSERO_RS05615 maleylacetoacetate isomerase

Query= reanno::psRCH2:GFF3446
         (219 letters)



>FitnessBrowser__HerbieS:HSERO_RS05615
          Length = 215

 Score =  233 bits (593), Expect = 3e-66
 Identities = 116/215 (53%), Positives = 149/215 (69%), Gaps = 5/215 (2%)

Query: 6   TLYGYWRSSAAYRVRIALNLKGLAYRQVPVHLVKDGGQQRAADYRALNPQQLVPLLVDEG 65
           TLY Y+RSSA+YRVRIAL+LK L Y  VPVHL+  GG+Q    +  +NP  LVP+L +EG
Sbjct: 3   TLYSYFRSSASYRVRIALHLKDLPYETVPVHLLNQGGEQLLPAFTEINPHALVPVLAEEG 62

Query: 66  NGGARISQSLAILEYLDEVFPVPALLPADPVERAQVRSLAMHIACEIHPLNNLRVLQYLS 125
           +    +SQSLA+LE L+E  P P+LLP D  +RA +R+L++ IAC+IHPLNNLRVL+YL 
Sbjct: 63  H---YVSQSLAMLELLEERHPTPSLLPGDAFQRAHIRALSLAIACDIHPLNNLRVLKYLK 119

Query: 126 AELGVDDEAKNAWYRHWVSQGLAAVEQGL--ETFGDKLSLNDRPGYLEACLVPQVYNARR 183
            ELG+DDE KNAW  HW++ G  A+E+ L  +T      + D P   + CLVPQ++NARR
Sbjct: 120 RELGMDDERKNAWIAHWINLGFTALERQLAADTTRGHFCVGDAPTMADCCLVPQIFNARR 179

Query: 184 FACDLAAYPRILEIVARCETLPAFQQAAPEVQPDA 218
           F  D+A YP +  I   C  LPAFQQA P  QPDA
Sbjct: 180 FEVDMAPYPTLCAIEQACHALPAFQQAHPAQQPDA 214


Lambda     K      H
   0.321    0.137    0.412 

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: 200
Number of extensions: 9
Number of successful extensions: 3
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: 219
Length of database: 215
Length adjustment: 22
Effective length of query: 197
Effective length of database: 193
Effective search space:    38021
Effective search space used:    38021
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: 45 (21.9 bits)

Align candidate HSERO_RS05615 HSERO_RS05615 (maleylacetoacetate isomerase)
to HMM TIGR01262 (maiA: maleylacetoacetate isomerase (EC 5.2.1.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.26381.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26381.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.