GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Escherichia coli BW25113

Align mannose-6-phosphate isomerase (EC 5.3.1.8) (characterized)
to candidate 15734 b1613 mannose-6-phosphate isomerase (VIMSS)

Query= ecocyc::MANNPISOM-MONOMER
         (391 letters)



>FitnessBrowser__Keio:15734
          Length = 391

 Score =  772 bits (1994), Expect = 0.0
 Identities = 391/391 (100%), Positives = 391/391 (100%)

Query: 1   MQKLINSVQNYAWGSKTALTELYGMENPSSQPMAELWMGAHPKSSSRVQNAAGDIVSLRD 60
           MQKLINSVQNYAWGSKTALTELYGMENPSSQPMAELWMGAHPKSSSRVQNAAGDIVSLRD
Sbjct: 1   MQKLINSVQNYAWGSKTALTELYGMENPSSQPMAELWMGAHPKSSSRVQNAAGDIVSLRD 60

Query: 61  VIESDKSTLLGEAVAKRFGELPFLFKVLCAAQPLSIQVHPNKHNSEIGFAKENAAGIPMD 120
           VIESDKSTLLGEAVAKRFGELPFLFKVLCAAQPLSIQVHPNKHNSEIGFAKENAAGIPMD
Sbjct: 61  VIESDKSTLLGEAVAKRFGELPFLFKVLCAAQPLSIQVHPNKHNSEIGFAKENAAGIPMD 120

Query: 121 AAERNYKDPNHKPELVFALTPFLAMNAFREFSEIVSLLQPVAGAHPAIAHFLQQPDAERL 180
           AAERNYKDPNHKPELVFALTPFLAMNAFREFSEIVSLLQPVAGAHPAIAHFLQQPDAERL
Sbjct: 121 AAERNYKDPNHKPELVFALTPFLAMNAFREFSEIVSLLQPVAGAHPAIAHFLQQPDAERL 180

Query: 181 SELFASLLNMQGEEKSRALAILKSALDSQQGEPWQTIRLISEFYPEDSGLFSPLLLNVVK 240
           SELFASLLNMQGEEKSRALAILKSALDSQQGEPWQTIRLISEFYPEDSGLFSPLLLNVVK
Sbjct: 181 SELFASLLNMQGEEKSRALAILKSALDSQQGEPWQTIRLISEFYPEDSGLFSPLLLNVVK 240

Query: 241 LNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEAKPANQ 300
           LNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEAKPANQ
Sbjct: 241 LNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEAKPANQ 300

Query: 301 LLTQPVKQGAELDFPIPVDDFAFSLHDLSDKETTISQQSAAILFCVEGDATLWKGSQQLQ 360
           LLTQPVKQGAELDFPIPVDDFAFSLHDLSDKETTISQQSAAILFCVEGDATLWKGSQQLQ
Sbjct: 301 LLTQPVKQGAELDFPIPVDDFAFSLHDLSDKETTISQQSAAILFCVEGDATLWKGSQQLQ 360

Query: 361 LKPGESAFIAANESPVTVKGHGRLARVYNKL 391
           LKPGESAFIAANESPVTVKGHGRLARVYNKL
Sbjct: 361 LKPGESAFIAANESPVTVKGHGRLARVYNKL 391


Lambda     K      H
   0.316    0.132    0.379 

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: 685
Number of extensions: 13
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: 391
Length of database: 391
Length adjustment: 31
Effective length of query: 360
Effective length of database: 360
Effective search space:   129600
Effective search space used:   129600
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate 15734 b1613 (mannose-6-phosphate isomerase (VIMSS))
to HMM TIGR00218 (manA: mannose-6-phosphate isomerase, class I (EC 5.3.1.8))

Software error:

../bin/blast/fastacmd -i /tmp/list.8111.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8111.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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