GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Desulfovibrio vulgaris Miyazaki F

Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate 8499455 DvMF_0227 phosphoglucomutase (RefSeq)

Query= CharProtDB::CH_002452
         (546 letters)



>FitnessBrowser__Miya:8499455
          Length = 549

 Score =  686 bits (1771), Expect = 0.0
 Identities = 341/547 (62%), Positives = 416/547 (76%), Gaps = 1/547 (0%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60
           MA H +AGQ  + S L+++  L A YY   P+    E  V FGTSGHRG A   SFNE H
Sbjct: 1   MATHPQAGQRPEASQLVDIPALVAAYYTEHPDTAAPERRVSFGTSGHRGGALSGSFNEEH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           ILA+ QA+ E RA+ GITGP ++G DTHALSEPA  + LEVLAANGV  ++Q+  G+TPT
Sbjct: 61  ILAVTQAVCEYRAQAGITGPLFLGMDTHALSEPAHRTALEVLAANGVSTVIQQGGGYTPT 120

Query: 121 PAVSNAILVHNK-KGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANA 179
           P +S+AIL  N  +   L DGIVITPSHNPPEDGG KYNPP+GGPADT+ TK ++ RAN 
Sbjct: 121 PVISHAILTWNAGRAQGLGDGIVITPSHNPPEDGGFKYNPPHGGPADTDATKWIQRRANE 180

Query: 180 LLADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGS 239
           LL DG + V+R+ L +A+A+  V ++D V+ +V  LA +VDM AI+ AGL LG DPLGGS
Sbjct: 181 LLDDGNRAVRRMHLRDALAAPCVSQRDFVRGYVADLASVVDMPAIKAAGLKLGADPLGGS 240

Query: 240 GIEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDL 299
            + YW  I E Y L++T+VND VD TFRFM LDKDG IRMDCSS  AMAGL+ LRDKFD+
Sbjct: 241 SLAYWHPIAEAYGLDITVVNDAVDPTFRFMPLDKDGKIRMDCSSPWAMAGLINLRDKFDV 300

Query: 300 AFANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVV 359
           AF ND D DRHGIVT +GLMNPNHYLAVA+ YLF+HRPQW    AVGKTLV+S+M+DRV 
Sbjct: 301 AFGNDADADRHGIVTASGLMNPNHYLAVAVWYLFRHRPQWSPQCAVGKTLVTSSMVDRVA 360

Query: 360 NDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAA 419
             LGRK+VEVPVGFKWFV  L +GS GFGGEESAGASFLR DGT W+TDKDG+++ LLAA
Sbjct: 361 ASLGRKVVEVPVGFKWFVQPLLEGSCGFGGEESAGASFLRRDGTVWTTDKDGLLLNLLAA 420

Query: 420 EITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPIT 479
           EI AV G++P E Y +L ++FGAP Y RLQ+ A + ++A L+ LSP++++A+ LAG PIT
Sbjct: 421 EIMAVEGRDPAELYTKLTEQFGAPLYERLQSPAGAERRAVLANLSPDVLTATELAGAPIT 480

Query: 480 ARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIV 539
           A LT APGN ASIGGLKV+TD+GWFAARPSGTED YKIY ESF G +H K+I++EAV+IV
Sbjct: 481 AMLTKAPGNDASIGGLKVITDDGWFAARPSGTEDMYKIYTESFKGSDHLKRIQQEAVDIV 540

Query: 540 SEVLKNA 546
                 A
Sbjct: 541 DRAFAAA 547


Lambda     K      H
   0.316    0.134    0.395 

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: 899
Number of extensions: 42
Number of successful extensions: 2
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: 546
Length of database: 549
Length adjustment: 36
Effective length of query: 510
Effective length of database: 513
Effective search space:   261630
Effective search space used:   261630
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: 53 (25.0 bits)

Align candidate 8499455 DvMF_0227 (phosphoglucomutase (RefSeq))
to HMM TIGR01132 (pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific (EC 5.4.2.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.18914.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18914.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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