GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Cupriavidus basilensis 4G11

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate RR42_RS35915 RR42_RS35915 beta-ketoadipyl CoA thiolase

Query= uniprot:B2SYZ2
         (400 letters)



>FitnessBrowser__Cup4G11:RR42_RS35915
          Length = 400

 Score =  629 bits (1623), Expect = 0.0
 Identities = 311/400 (77%), Positives = 352/400 (88%)

Query: 1   MNDAFICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQA 60
           M +AFICDAIRTPIGRY G+L  VR DDLGAVP+KAL+ RNP +DW  +DDVIYG ANQA
Sbjct: 1   MTEAFICDAIRTPIGRYAGSLSGVRPDDLGAVPLKALMARNPNLDWSAIDDVIYGNANQA 60

Query: 61  GEDNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESM 120
           GEDNRNVARMS LLAGLP   PG+TINRLCGSGMDA GTAARAIK+GEA LM+AGGVESM
Sbjct: 61  GEDNRNVARMSLLLAGLPQSVPGATINRLCGSGMDATGTAARAIKSGEAGLMLAGGVESM 120

Query: 121 TRAPFVMGKATSAFARQADIYDTTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRAD 180
           +RAPFVMGKATSAF+R A I+DTTIGWRFINP M+  YGVDSMPETAENVA ++ +SR D
Sbjct: 121 SRAPFVMGKATSAFSRDAQIFDTTIGWRFINPAMRAAYGVDSMPETAENVATDYKISRED 180

Query: 181 QDAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPRETSLESLGKLKGV 240
           QD  AL SQ+KA+RAQ DGTLAQEI  V IAQKKGDP+    DEHPR TS+E+LGKL+GV
Sbjct: 181 QDLMALRSQEKASRAQADGTLAQEITAVTIAQKKGDPLVVERDEHPRATSMEALGKLRGV 240

Query: 241 VRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARVVGMATAGVEPRIMGIGPAP 300
           VR DG+VTAGNASGVNDGACA+LLA++ AA Q+GL  +AR+VGMATAGV PR+MGIGPAP
Sbjct: 241 VRADGTVTAGNASGVNDGACAILLASEAAARQHGLTPKARIVGMATAGVAPRVMGIGPAP 300

Query: 301 ATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGHPLGA 360
           A+QKLLKQLGMT++Q+DVIELNEAFA+QGLAVLR LG+ DDD RVNPNGGAIALGHPLG 
Sbjct: 301 ASQKLLKQLGMTIDQMDVIELNEAFAAQGLAVLRELGVADDDARVNPNGGAIALGHPLGM 360

Query: 361 SGARLITTALYQLERTNGRFALCTMCIGVGQGIALVIERL 400
           SGARL+TTA+YQL RT GR+ALCTMCIGVGQGIA+VIER+
Sbjct: 361 SGARLVTTAMYQLHRTGGRYALCTMCIGVGQGIAMVIERV 400


Lambda     K      H
   0.318    0.135    0.386 

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: 588
Number of extensions: 17
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate RR42_RS35915 RR42_RS35915 (beta-ketoadipyl CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

Software error:

../bin/blast/fastacmd -i /tmp/list.31171.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.31171.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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