GapMind for catabolism of small carbon sources

 

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

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_011383790.1 AMB_RS06985 fructose-bisphosphate aldolase class II

Query= BRENDA::Q602L6
         (354 letters)



>NCBI__GCF_000009985.1:WP_011383790.1
          Length = 354

 Score =  523 bits (1347), Expect = e-153
 Identities = 255/353 (72%), Positives = 300/353 (84%)

Query: 1   MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60
           M+L+S+RQLLDHAAE+ YG+PAFNVNNMEQ+KAIMEAASA DAPVILQ SAGAR YAGEP
Sbjct: 1   MSLVSMRQLLDHAAENSYGIPAFNVNNMEQVKAIMEAASACDAPVILQASAGARKYAGEP 60

Query: 61  FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120
           FLRHL+ AAIE YP IPVCMHQDHG SPA+ +R+IQSGFSSVMMDGSL ED KTP+ + Y
Sbjct: 61  FLRHLILAAIEAYPQIPVCMHQDHGTSPAINVRAIQSGFSSVMMDGSLREDGKTPSDWDY 120

Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180
           NV  T++VV++AHACGVSVEGELGCLGSLETG AGKEDG GAEG+LDHS LLTDPDEAA+
Sbjct: 121 NVAVTKQVVDIAHACGVSVEGELGCLGSLETGTAGKEDGVGAEGKLDHSQLLTDPDEAAE 180

Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240
           FV+ TQVDALAIAIGTSHGAYKFTR PTG+VL I R+K IH RIP  HLVMHGSSSVP++
Sbjct: 181 FVKLTQVDALAIAIGTSHGAYKFTRPPTGEVLAIKRIKEIHARIPNTHLVMHGSSSVPQD 240

Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300
             +++NDYGG +G+TYGVPV EIVEGI+HGVRK+NIDTDLR+A  G +R++  ++ K FD
Sbjct: 241 LLKIVNDYGGALGETYGVPVGEIVEGIKHGVRKINIDTDLRLAVTGCIRKYFHDNPKKFD 300

Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKLDPIV 353
           PR   K +  AM  +C++RY+AFG +GQA+KIK + LEDMS  YA+G L P V
Sbjct: 301 PRDYLKPSIAAMVEVCKSRYDAFGTSGQASKIKVVGLEDMSALYAKGALAPKV 353


Lambda     K      H
   0.320    0.134    0.391 

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: 507
Number of extensions: 21
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: 354
Length of database: 354
Length adjustment: 29
Effective length of query: 325
Effective length of database: 325
Effective search space:   105625
Effective search space used:   105625
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: 49 (23.5 bits)

Align candidate WP_011383790.1 AMB_RS06985 (fructose-bisphosphate aldolase class II)
to HMM TIGR01521 (fba: fructose-bisphosphate aldolase, class II, Calvin cycle subtype (EC 4.1.2.13))

Software error:

../bin/blast/fastacmd -i /tmp/list.19361.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19361.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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