GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Pseudomonas fluorescens FW300-N2E3

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate AO353_21350 AO353_21350 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::G5CZI2
         (498 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21350
          Length = 500

 Score =  623 bits (1606), Expect = 0.0
 Identities = 304/496 (61%), Positives = 384/496 (77%), Gaps = 3/496 (0%)

Query: 4   IGHLINGQLV-TENTRSQNVFNPATGEIGKQLDLASTKTVEQAISAAQHAFPTWRNTPPL 62
           IGH +NGQ+  T + R  NVFNPATG I  ++ LAS +TV++A+++A  AFP W     L
Sbjct: 7   IGHYLNGQVQDTGSERFSNVFNPATGAIQARVGLASQQTVDEAVASALRAFPAWSEQSSL 66

Query: 63  KRARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLKGEH 122
           +R+RVMF+FKELL++H +E+  +I  EHGK+  DA GE+ RGIE VEYACGAP LLK E 
Sbjct: 67  RRSRVMFKFKELLDRHHNELAEIISREHGKVFSDAKGEVTRGIEIVEYACGAPNLLKTEF 126

Query: 123 SRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPSSTL 182
           S N+G GID+W+  QP+GV AG+TPFNFPVMVPLWM P+A+V GNCF+LKPSERDPS++L
Sbjct: 127 SDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVTGNCFILKPSERDPSASL 186

Query: 183 YIAQLLQEAGLPDGVMNVVNGDKEAVDALLHDDRVKAVSFVGSTPIAEYIYRTASANGKR 242
            +A+LL EAGLPDGV +VV GDK AVDALL    ++A+SFVGSTPIAEYI++ A+A GKR
Sbjct: 187 LMARLLTEAGLPDGVFSVVQGDKSAVDALLQHPDIEAISFVGSTPIAEYIHQQATARGKR 246

Query: 243 CQALGGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAAGDALVSKMT 302
            QALGGAKNH IVMPDAD+D A + L+GAAFGS+GERCMA+S+AVAVGD  GD L++K+ 
Sbjct: 247 VQALGGAKNHMIVMPDADLDQAADALIGAAFGSAGERCMAISIAVAVGD-VGDKLIAKLL 305

Query: 303 QAMQKLKVGPSTDSGNDFGPVITRQHQEKVIGYINSAEQQGATIVVDGRQPKVPNHENGF 362
             + +LKVG      +D GP++T +H+ KV G+I+    QGA ++VDGR  KVP  ENGF
Sbjct: 306 PRIDQLKVGNGMQGDSDMGPLVTAEHKAKVEGFIDQGVAQGAQLIVDGRGFKVPGAENGF 365

Query: 363 FVGGTLIDHVTPEMTSYQEEIFGPVLQVVRVATMQDAMDLIDAHEYGNGTCIFTRDGEAA 422
           FVG TL D VT EM+ YQ+EIFGPVL +VRVA    A+ LI+AHE+GNG   FT DG  A
Sbjct: 366 FVGATLFDKVTTEMSIYQQEIFGPVLGIVRVADFASAVALINAHEFGNGVSCFTSDGGIA 425

Query: 423 RYFSDNIQVGMVGINIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTVTQRWP 482
           R F+  I+VGMVGIN+P+PVP+A+HSFGGWKRSLFGD HAYG + +RFY++ K+V QRWP
Sbjct: 426 RAFARTIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGIRFYSRYKSVMQRWP 485

Query: 483 SAGVREGAEFSMPTMK 498
            + + +G EFSMPT K
Sbjct: 486 DS-IAKGPEFSMPTAK 500


Lambda     K      H
   0.319    0.135    0.405 

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: 726
Number of extensions: 24
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: 498
Length of database: 500
Length adjustment: 34
Effective length of query: 464
Effective length of database: 466
Effective search space:   216224
Effective search space used:   216224
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate AO353_21350 AO353_21350 (methylmalonate-semialdehyde dehydrogenase)
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.16725.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16725.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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