GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Herbaspirillum seropedicae SmR1

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate HSERO_RS13360 HSERO_RS13360 phosphoglucomutase

Query= BRENDA::A0A0H3NJ17
         (546 letters)



>FitnessBrowser__HerbieS:HSERO_RS13360
          Length = 549

 Score =  616 bits (1589), Expect = 0.0
 Identities = 314/545 (57%), Positives = 395/545 (72%), Gaps = 2/545 (0%)

Query: 2   AIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAGRHSFNEPHI 61
           +++  AGQ A  S L+++  L + YY L+P+   A H V FGTSGHRG+A  HSFNE H+
Sbjct: 3   SVNPLAGQRAAPSALVDLPVLVSNYYSLRPDVAEASHRVAFGTSGHRGNANAHSFNEWHV 62

Query: 62  LAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPTP 121
           LAI QAI + R + G  GP ++G DTHALSEPA+ S LEVLAAN V  ++ E + + PTP
Sbjct: 63  LAITQAICDYRKEQGFKGPLFLGIDTHALSEPAWHSALEVLAANEVVTMLAEGSPYAPTP 122

Query: 122 AVSNAILVHNK-KGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANAL 180
           AVS+AIL HN+     LADGIV+TPSHNPP++GG KYN PNGGP+D+NVT  +E RANA 
Sbjct: 123 AVSHAILTHNRVHRDALADGIVVTPSHNPPDNGGFKYNMPNGGPSDSNVTGWIEQRANAY 182

Query: 181 LAGGLQGVKRISLDAAMASGHVKAVDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGSG 240
           L   LQGV+R+S + A+ +   +  D +  +V  L +I+D+AAI  A + +GVDPLGG+G
Sbjct: 183 LEQQLQGVRRVSFEKALKADTTRRYDYLDNYVSDLPNIIDLAAISGANVKIGVDPLGGAG 242

Query: 241 IEYWKRIAEHYKLNLTLVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA 300
           + YW  IA+ YKLNL +VN +VD TFRF+ LD D  IRMD SS  AM+ L+AL+D+FD+A
Sbjct: 243 LHYWSAIADRYKLNLEVVNTEVDATFRFVPLDWDAQIRMDPSSPHAMSELIALKDRFDVA 302

Query: 301 FANDPDYDRHGIVTPA-GLMNPNHYLAVAINYLFQHRPLWGKDVAVGKTLVSSAMIDRVV 359
            A D D+DRHGIV  + GLM  N YL+VA+ YLF+HRP W  D A+GKTLVSS MI+RV 
Sbjct: 303 MACDTDHDRHGIVAKSRGLMPANDYLSVAVYYLFRHRPAWRADAAIGKTLVSSQMINRVA 362

Query: 360 NDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAA 419
             L RKL+E+PVGFKWFVDGL+DGS  FG EESAGASF+RFDG PWSTDKDGI   LLAA
Sbjct: 363 KHLERKLLEMPVGFKWFVDGLYDGSLAFGCEESAGASFVRFDGQPWSTDKDGITAALLAA 422

Query: 420 EITAVTGKNPQEHYNELAARFGAPSYNRLQASATSAQKAALSKLSPEMVSASTLAGDPIT 479
           E+TA TG +P + Y +L  + GAP   R +A+AT  QKA LSKLSP+ VS++ LAG+PI 
Sbjct: 423 EMTARTGNDPGQIYEDLTHQLGAPLNGRKEAAATPEQKARLSKLSPQDVSSTELAGEPIR 482

Query: 480 ARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIV 539
             LT AP NG   GGLK++TDNGWFAARPSGTE  YKIY ESF  + H  +I  EA +IV
Sbjct: 483 EVLTTAPANGKPFGGLKIVTDNGWFAARPSGTESIYKIYGESFRDQAHLDKIFAEAQDIV 542

Query: 540 SEVLK 544
           +  L+
Sbjct: 543 TRALQ 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: 895
Number of extensions: 38
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: 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 HSERO_RS13360 HSERO_RS13360 (phosphoglucomutase)
to HMM TIGR01132 (pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific (EC 5.4.2.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.20854.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20854.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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