GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Cupriavidus basilensis 4G11

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate RR42_RS15595 RR42_RS15595 acetoacetyl-CoA synthetase

Query= BRENDA::D6EQU8
         (658 letters)



>FitnessBrowser__Cup4G11:RR42_RS15595
          Length = 678

 Score =  640 bits (1652), Expect = 0.0
 Identities = 315/666 (47%), Positives = 426/666 (63%), Gaps = 17/666 (2%)

Query: 4   ENPQPLWQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTEWF 63
           E  Q  W P       +RI  F  W     G  A   Y AL +WSV +L+ FW A+  +F
Sbjct: 5   EEGQLRWTPSQAFRDGSRIAHFMRWLESERGL-AFADYGALWQWSVTDLEAFWDAIRAYF 63

Query: 64  DVRFSTPYARVLGDRTMPGAQWFPGATLNYAEHALRAAGTRP--DEPALLYVDETHEPAP 121
           D+RF TP  RVLG   MPGA+WF GA+LNY +   R AG+    +  A+ Y  E+     
Sbjct: 64  DLRFDTPAERVLGSAQMPGARWFEGASLNYVQQVFRHAGSGAARERTAIRYAGESIAVTD 123

Query: 122 VTWAELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDFG 181
           ++W  L +QVASLA  LR +GV  GDRV+GYLPNIP  VVA LATA++G +W+ CAPD G
Sbjct: 124 LSWDVLEQQVASLAHALRGMGVARGDRVAGYLPNIPATVVAFLATASLGAIWSGCAPDMG 183

Query: 182 ARSVLDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGTEA-- 239
             +V DRF+Q+EP VL  VDGYRYGGK +DR   +A+L   LP+L  ++ +P   T+A  
Sbjct: 184 QVAVSDRFRQIEPKVLIAVDGYRYGGKAYDRAPVLADLAAALPSLTDLVLVPGEHTDAHA 243

Query: 240 -PDGTL--------DWETLTAADAEPVYEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGIL 290
            P+            W+ + A       E VPFDHPLW++YSSGTTG+PK IV   GGI+
Sbjct: 244 APNAIALPANVRRHAWQAVLAHRVPLAIESVPFDHPLWIVYSSGTTGMPKPIVHGHGGIV 303

Query: 291 VEHLKQLGLHCDLGPGDRFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGFPATDAQWR 350
           +E LK +  H +LGP D F WY+S+GW+MWN  ++GLL G+TI LYDG+P +P     WR
Sbjct: 304 IEQLKLMAFHNNLGPDDVFHWYSSSGWIMWNAQIAGLLLGSTIALYDGNPAWPDAGVLWR 363

Query: 351 IAERTGATLFGTSAAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAA 410
             +    T FG  AA+  A  KAG+ PAR  DLS ++ + +TGSPLP + + W++   +A
Sbjct: 364 FVDAARVTAFGAGAAFFTAGMKAGIEPARVADLSRLRALGSTGSPLPAEAYDWIYRHVSA 423

Query: 411 GGADLWIASVSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEVGEL 470
              D+W+A +SGGTD    F    P LPV+ GE+Q   LG  ++++D +G+ L  EVGEL
Sbjct: 424 ---DIWLAPMSGGTDFAGSFVAGCPILPVYSGEMQCRCLGAKVEAFDEAGNALVGEVGEL 480

Query: 471 VVTNPMPSMPIRFWNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLNR 530
           V T PMPSMP+  W D +G RY DSYFDTYPGVWRHGDWI +T+ G  +I+GRSD+T+NR
Sbjct: 481 VCTAPMPSMPLFLWGDTNGQRYRDSYFDTYPGVWRHGDWIKITAHGGAIIYGRSDATINR 540

Query: 531 QGVRMGSADIYEAVERLPEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIKRT 590
            G+RMG++++Y  VE LPE+ +S+V+ +E      +MPLFV L  G  LDDAL D ++  
Sbjct: 541 HGIRMGTSELYRVVEDLPEVLDSMVVDLEYLGRDSYMPLFVVLREGMVLDDALRDTMRAR 600

Query: 591 IRVNLSPRHVPDEVIEVPGIPHTLTGKRIEVPVKRLLQGTPLDKAVNPGSIDNLDLLHFY 650
           IR  LS RHVP+E+++VPG+P TL+GK++EVP+K+LL G   DK  N  ++ N + L +Y
Sbjct: 601 IRSALSSRHVPNEILQVPGVPRTLSGKKMEVPIKKLLLGHAPDKIANRDAMANPETLDWY 660

Query: 651 EELARK 656
              A +
Sbjct: 661 FAYAER 666


Lambda     K      H
   0.320    0.138    0.442 

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: 1482
Number of extensions: 71
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: 658
Length of database: 678
Length adjustment: 38
Effective length of query: 620
Effective length of database: 640
Effective search space:   396800
Effective search space used:   396800
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: 54 (25.4 bits)

Align candidate RR42_RS15595 RR42_RS15595 (acetoacetyl-CoA synthetase)
to HMM TIGR01217 (acetoacetate-CoA ligase (EC 6.2.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.15328.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15328.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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