GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Phaeobacter inhibens BS107

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate GFF398 PGA1_c04090 beta-ketoadipyl-CoA thiolase PaaJ

Query= uniprot:D8ITH5
         (401 letters)



>FitnessBrowser__Phaeo:GFF398
          Length = 400

 Score =  560 bits (1442), Expect = e-164
 Identities = 278/400 (69%), Positives = 321/400 (80%)

Query: 1   MEALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAG 60
           M+A ICDA RTP GRYGGAL  +R DDLAA PI +L  RNP VDWS ++D++ G ANQAG
Sbjct: 1   MDAFICDATRTPIGRYGGALSQLRTDDLAALPIAALAARNPDVDWSSLDDVILGDANQAG 60

Query: 61  EDNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMT 120
           E NRNVARMA LLAGLP  VPG+T+NRLC S +DAVGMA+R IK+G+  + IAGGVESM+
Sbjct: 61  ESNRNVARMAALLAGLPTTVPGTTINRLCASGMDAVGMASRGIKAGDYDMAIAGGVESMS 120

Query: 121 RAPFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ 180
           RAPFVM KA SAF R+ A++DTTIGWRFVN  M   YG DSMP+TA+NVA D+ I+R DQ
Sbjct: 121 RAPFVMPKATSAFTRANAVYDTTIGWRFVNKKMHEMYGTDSMPQTADNVAEDYGISREDQ 180

Query: 181 DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGV 240
           DAFA RSQ RWAAA  AG F  EI P+TIPQ+KGD LVV TDEHPRP T+   LA LKGV
Sbjct: 181 DAFAARSQARWAAAHEAGIFNDEITPVTIPQRKGDDLVVDTDEHPRPGTSAEKLAGLKGV 240

Query: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300
             PD +VTAGNASGVNDGA A+L+A+  AA    LKP AR++GM  AGV PRIMG GP P
Sbjct: 241 NGPDKSVTAGNASGVNDGAAAILMANEAAAAKNGLKPMARIVGMTAAGVEPRIMGIGPVP 300

Query: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360
           A RKVLA+ GLT+ QMDVIELNEAFA+QGLA +R+LG+ DDA HVNPNGGAIA+GHPLG 
Sbjct: 301 ATRKVLARTGLTIDQMDVIELNEAFASQGLATLRELGVADDAPHVNPNGGAIALGHPLGM 360

Query: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400
           SGARLV TA  QL+R+GGRYALCTMC+GVGQG AL++ERV
Sbjct: 361 SGARLVLTAAYQLQRTGGRYALCTMCVGVGQGTALILERV 400


Lambda     K      H
   0.320    0.135    0.394 

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: 553
Number of extensions: 16
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: 401
Length of database: 400
Length adjustment: 31
Effective length of query: 370
Effective length of database: 369
Effective search space:   136530
Effective search space used:   136530
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: 50 (23.9 bits)

Align candidate GFF398 PGA1_c04090 (beta-ketoadipyl-CoA thiolase PaaJ)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

Software error:

../bin/blast/fastacmd -i /tmp/list.21682.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21682.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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