GapMind for catabolism of small carbon sources

 

Alignments for a candidate for speB in Azospirillum brasilense Sp245

Align agmatinase (EC 3.5.3.11) (characterized)
to candidate AZOBR_RS30775 AZOBR_RS30775 agmatinase

Query= BRENDA::W5PHZ9
         (361 letters)



>FitnessBrowser__azobra:AZOBR_RS30775
          Length = 351

 Score =  244 bits (624), Expect = 2e-69
 Identities = 137/318 (43%), Positives = 197/318 (61%), Gaps = 19/318 (5%)

Query: 44  QASDGPRNQPPSSEFVARSVGICSMMRLPMQ------ATPEGLDAALVGVPLDIGTSNRP 97
           Q S G R QP          G+ +++  P +      A   GLD AL+GVP+D+G +NR 
Sbjct: 34  QFSGGKRVQP--------FAGVSTLLDAPYRPDAADAADFGGLDIALIGVPMDLGVTNRA 85

Query: 98  GARFGPRRIREESVMLRTANPSTGAVPFQFLKVADLGDVNVNLYNLQDSCRL-IRADYQK 156
           GAR GPR +R     +     +   VP    K+AD+GDV ++     ++C   I A Y +
Sbjct: 86  GARLGPRAVRGME-RIGPYEHALRMVPAASCKLADVGDVPLSSRFSLEACHGDILAFYNR 144

Query: 157 IVAAGCVPLTLGGDHTITYPILQAIAEKHGPVGLVHVDAHMDTADKALGEKLYHGTPFRR 216
           ++ AG VPL++GGDH+ITY IL+A+  +  PVG++H DAH DT     G K +HG PFR+
Sbjct: 145 VMDAGVVPLSVGGDHSITYSILKALGRER-PVGMIHFDAHCDTGGPYEGAKFHHGGPFRQ 203

Query: 217 CVDEGLLDCKRVVQIGIRGSSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMG 276
            V +G+LD +R VQIGIRGS+  L  + +S   G  V+ AED   + +  ++   R+ +G
Sbjct: 204 AVLDGVLDPERTVQIGIRGSTEYL--WEFSYDSGMTVIHAEDIPERGIASVIETARKVVG 261

Query: 277 GRPIYISFDIDGLDPAYAPGTGTPEIAGLTPSQALEIIRGCQGLNVVGCDLVEVSPPYDP 336
             P+Y+SFD+D LDP +APGTGTPE+ GLT  +AL I+RG  GL+++G D+VEV+P YD 
Sbjct: 262 DGPVYVSFDVDCLDPVFAPGTGTPEVGGLTTREALAILRGLDGLDIIGGDVVEVAPQYDA 321

Query: 337 SGNTALVAANLLFEMLCV 354
           + NTA   A +LFE+LC+
Sbjct: 322 TTNTAHAGAQMLFEILCL 339


Lambda     K      H
   0.321    0.139    0.426 

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: 444
Number of extensions: 27
Number of successful extensions: 4
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: 361
Length of database: 351
Length adjustment: 29
Effective length of query: 332
Effective length of database: 322
Effective search space:   106904
Effective search space used:   106904
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 AZOBR_RS30775 AZOBR_RS30775 (agmatinase)
to HMM TIGR01230 (speB: agmatinase (EC 3.5.3.11))

Software error:

../bin/blast/fastacmd -i /tmp/list.12629.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12629.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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