GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvT in Caulobacter crescentus NA1000

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate CCNA_03465 CCNA_03465 glycine cleavage system aminomethyltransferase T

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1866
         (374 letters)



>FitnessBrowser__Caulo:CCNA_03465
          Length = 375

 Score =  369 bits (948), Expect = e-107
 Identities = 200/372 (53%), Positives = 242/372 (65%), Gaps = 5/372 (1%)

Query: 2   STEQLLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQIR 61
           S + L KTPL+  H+  GARMVPFAGY MPVQY  GV+KEH  TR+ AGLFDVSHMGQ R
Sbjct: 7   SDQDLKKTPLYDAHVAAGARMVPFAGYSMPVQYKDGVLKEHLWTREHAGLFDVSHMGQAR 66

Query: 62  LTGANAAKALETLVPVDIIDLPVGMQRYAMFTNATGGILDDLMVANLGNDELFLVVNAAC 121
           + G N AK+ E +V  D   L  G QRY +  NA GGI+DDLM A    D LF+VVN AC
Sbjct: 67  IRGENPAKSFEKVVSADYQGLKAGKQRYGVLLNADGGIVDDLMTARPDEDGLFVVVNGAC 126

Query: 122 KDQDLAHLRKHIGDQCTIEPLFEERALLALQGPAAVTVLARLAPEVAKMTFMQFARVKLL 181
           KD D A + + +  + T+  L E+RALLALQGP A  VLA   PE A+M FM    +   
Sbjct: 127 KDNDYAIIARELAGEATVTRL-EDRALLALQGPEAAAVLAAHVPEAAQMVFMDAKALSAF 185

Query: 182 GVDCFVSRSGYTGEDGFEISVPATNAEALARALLAEAEVAAIGLGARDSLRLEAGLCLYG 241
           GVD  +SRSGYTGEDG+EISVPA  AE +   LLA+  V  IGLGARDSLRLEAGL LYG
Sbjct: 186 GVDAIISRSGYTGEDGYEISVPADAAERVWNTLLADERVKPIGLGARDSLRLEAGLPLYG 245

Query: 242 HDMNTDTTPIEASLLWAISKPRRADGARAGGFPGAETVFAQQQAGVSRKRVGLLPQERTP 301
           HD++   +PIEA L +A+ + RR     AG + GA  +  +    +SR RV L   E  P
Sbjct: 246 HDLDETVSPIEAGLNFAVGRSRR----EAGDYLGAARIAKELAGELSRVRVNLKVLEGAP 301

Query: 302 VREGAEIVNEAGDIIGSVCSGGFGPTLGGPLAMGYVDSAYIALDTPVWAIVRGKKVPLLV 361
            REGAEI +EAG++IG V SGGF P+LG P+A+G+   AY A+ T +  IVRGK     V
Sbjct: 302 AREGAEIADEAGNVIGKVTSGGFAPSLGFPIAIGFAPPAYAAVGTKLKVIVRGKPAAAEV 361

Query: 362 SKMPFVPQRYYR 373
              PFVP RY R
Sbjct: 362 VASPFVPNRYVR 373


Lambda     K      H
   0.321    0.138    0.405 

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: 420
Number of extensions: 19
Number of successful extensions: 3
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: 374
Length of database: 375
Length adjustment: 30
Effective length of query: 344
Effective length of database: 345
Effective search space:   118680
Effective search space used:   118680
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 CCNA_03465 CCNA_03465 (glycine cleavage system aminomethyltransferase T)
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))

Software error:

../bin/blast/fastacmd -i /tmp/list.1816.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1816.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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