GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Desulfovibrio vulgaris Hildenborough

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate 206872 DVU1428 phosphoglucomutase, alpha-D-glucose phosphate-specific

Query= BRENDA::A0A0H3NJ17
         (546 letters)



>MicrobesOnline__882:206872
          Length = 551

 Score =  659 bits (1699), Expect = 0.0
 Identities = 328/547 (59%), Positives = 406/547 (74%), Gaps = 1/547 (0%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAGRHSFNEPH 60
           M++H  AG+      L+N+  L  +YY   P+    E  V FGTSGHRGS+   +FNE H
Sbjct: 1   MSVHPLAGERPSHDRLVNIPALMGEYYTGHPDTTAVERRVAFGTSGHRGSSLHGTFNEEH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           ILA+ QA+ + R ++GI GP ++G DTHALSE A  + LEVLAANGV+V +Q   GFTPT
Sbjct: 61  ILAVTQAVCDIRREDGIAGPLFLGMDTHALSECAHRTALEVLAANGVNVRLQTGGGFTPT 120

Query: 121 PAVSNAILVHNK-KGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANA 179
           P +S+AIL  N  +  P ADG+VITPSHNPPEDGG KYNPP+GGPADT VT+ +E RAN 
Sbjct: 121 PVISHAILCWNAHRDRPRADGVVITPSHNPPEDGGFKYNPPHGGPADTTVTRRIERRANE 180

Query: 180 LLAGGLQGVKRISLDAAMASGHVKAVDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGS 239
           LL  GL GV+R+ L  A+ +  ++AVDLV  +V  LA ++DM AI+ AGL +  DPLGGS
Sbjct: 181 LLDNGLAGVRRVVLHKALRTPGIEAVDLVSAYVNDLASVLDMDAIRGAGLRIAADPLGGS 240

Query: 240 GIEYWKRIAEHYKLNLTLVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDL 299
            + YW  IAE Y L++T+VN + D TFRFM  DKDG +RMDCSS  AM GL+ LR  +D+
Sbjct: 241 SLAYWDPIAEKYGLDITVVNREADPTFRFMPQDKDGKVRMDCSSPWAMRGLIDLRQSYDI 300

Query: 300 AFANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPLWGKDVAVGKTLVSSAMIDRVV 359
           AF NDPD DRHGIVT  GL+NPNHY+A A+ YL++HRP W     +GKTLV+S+M+DRV 
Sbjct: 301 AFGNDPDADRHGIVTAQGLLNPNHYIAAAVWYLYRHRPGWNTTCGIGKTLVTSSMVDRVA 360

Query: 360 NDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAA 419
             LGRK+VEVPVGFKWFV  L DGS GFGGEESAGASFLR DGTPWSTDKDGIIM LLAA
Sbjct: 361 KLLGRKVVEVPVGFKWFVPLLLDGSCGFGGEESAGASFLRSDGTPWSTDKDGIIMNLLAA 420

Query: 420 EITAVTGKNPQEHYNELAARFGAPSYNRLQASATSAQKAALSKLSPEMVSASTLAGDPIT 479
           E+ AV  ++P E Y EL  R G P Y RLQ+ AT+AQ+A  + L+PE V A++LAG PIT
Sbjct: 421 EMMAVEERSPSEIYAELTERCGTPYYERLQSPATAAQRAVFAGLTPERVKATSLAGAPIT 480

Query: 480 ARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIV 539
           A LT APGNGA+IGGLKV+TD+GWFAARPSGTED YKIY ESF+  EH ++I+K+AV+IV
Sbjct: 481 AMLTHAPGNGAAIGGLKVVTDDGWFAARPSGTEDMYKIYTESFVSPEHLQRIQKDAVDIV 540

Query: 540 SEVLKNA 546
           + +  +A
Sbjct: 541 ASIFADA 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: 950
Number of extensions: 32
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: 551
Length adjustment: 36
Effective length of query: 510
Effective length of database: 515
Effective search space:   262650
Effective search space used:   262650
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 206872 DVU1428 (phosphoglucomutase, alpha-D-glucose phosphate-specific)
to HMM TIGR01132 (pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific (EC 5.4.2.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.7871.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7871.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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