GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Magnetospirillum magneticum AMB-1

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_011384541.1 AMB_RS10825 cyclohexa-1,5-dienecarbonyl-CoA hydratase

Query= BRENDA::O87873
         (258 letters)



>NCBI__GCF_000009985.1:WP_011384541.1
          Length = 259

 Score =  337 bits (865), Expect = 1e-97
 Identities = 174/254 (68%), Positives = 204/254 (80%)

Query: 5   SSPLKVWLERDGSLLRLRLARPKANIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPHF 64
           S+ LKVW +R+G LLRLRL+RPKANIVDA MIAA+  ALG+  +  ALRAVL+D EGPHF
Sbjct: 6   SNCLKVWKDREGKLLRLRLSRPKANIVDAEMIAALSAALGDAHEDSALRAVLIDHEGPHF 65

Query: 65  SFGASVDEHMPDQCAQMLKSLHGLVREMLDSPVPILVALRGQCLGGGLEVAAAGNLLFAA 124
           SFGASV EHMPDQCA ML SLH LV  M+D P+PILVA+RGQCLGGGLEVA AG+++F +
Sbjct: 66  SFGASVAEHMPDQCAAMLASLHKLVIAMVDFPLPILVAVRGQCLGGGLEVALAGHMMFVS 125

Query: 125 PDAKFGQPEIRLGVFAPAASCLLPPRVGQACAEDLLWSGRSIDGAEGHRIGLIDVLAEDP 184
           PDAK GQPEI LGVFAPAASCLLP R+ +  AEDLL+SGRSIDGAE  R+G+ + + +DP
Sbjct: 126 PDAKLGQPEIVLGVFAPAASCLLPERMPRVAAEDLLYSGRSIDGAEAARLGIANAVVDDP 185

Query: 185 EAAALRWFDEHIARLSASSLRFAVRAARCDSVPRIKQKLDTVEALYLEELMASHDAVEGL 244
           E AAL WFD   A+ SA+SLRFAV+AAR     R+K K+  VEALYL  LMA+HDAVEGL
Sbjct: 186 ENAALAWFDNGPAKHSAASLRFAVKAARLGMNERVKAKIAEVEALYLNGLMATHDAVEGL 245

Query: 245 KAFLEKRSANWENR 258
            AFLEKR A WE+R
Sbjct: 246 NAFLEKRPALWEDR 259


Lambda     K      H
   0.321    0.135    0.402 

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: 277
Number of extensions: 13
Number of successful extensions: 1
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: 258
Length of database: 259
Length adjustment: 24
Effective length of query: 234
Effective length of database: 235
Effective search space:    54990
Effective search space used:    54990
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 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate WP_011384541.1 AMB_RS10825 (cyclohexa-1,5-dienecarbonyl-CoA hydratase)
to HMM TIGR03189 (cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100))

Software error:

../bin/blast/fastacmd -i /tmp/list.1067.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1067.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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