GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutH in Pseudomonas fluorescens FW300-N1B4

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate Pf1N1B4_1581 Histidine ammonia-lyase (EC 4.3.1.3)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_320
         (510 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1581
          Length = 510

 Score =  955 bits (2469), Expect = 0.0
 Identities = 494/510 (96%), Positives = 505/510 (99%)

Query: 1   MTALNLIPGQLTLAQLRDVYQQPVKLTLDNSASAQIEASVACVEQILAENRTAYGINTGF 60
           MTALNLIPGQL+LAQLRDVYQQPVK+TLDNSASAQIEASVACVEQILAENRTAYGINTGF
Sbjct: 1   MTALNLIPGQLSLAQLRDVYQQPVKITLDNSASAQIEASVACVEQILAENRTAYGINTGF 60

Query: 61  GLLASTRIASEDLENLQRSLVLSHAAGVGQPISDELVRLIMVLKVNSLSRGFSGIRRVVI 120
           GLLASTRIASEDLENLQRSLVLSHAAGVG+PISD LVRL+MVLKVNSLSRGFSGIRRVVI
Sbjct: 61  GLLASTRIASEDLENLQRSLVLSHAAGVGEPISDALVRLVMVLKVNSLSRGFSGIRRVVI 120

Query: 121 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWMEATEALKVAG 180
           DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWMEATEALKVAG
Sbjct: 121 DALIALINAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGEWMEATEALKVAG 180

Query: 181 LTPLTLAAKEGLALLNGTQVSTAFALRGLFEGEDLFAGALALGGLTVEAVLGSRSPFDAR 240
           LTPLTLAAKEGLALLNGTQVSTA+ALRGLFEGEDLFAGALA+GG+TVEAVLGSRSPFDAR
Sbjct: 181 LTPLTLAAKEGLALLNGTQVSTAYALRGLFEGEDLFAGALAIGGMTVEAVLGSRSPFDAR 240

Query: 241 IHAARGQKGQIDAAAAYRDLLGERSEVSDSHENCEKVQDPYSLRCQPQVMGACLTQFRQA 300
           IHAARGQKGQIDAAAAYRDLLGERSEVSDSH+NCEKVQDPYSLRCQPQVMGACLTQFRQA
Sbjct: 241 IHAARGQKGQIDAAAAYRDLLGERSEVSDSHQNCEKVQDPYSLRCQPQVMGACLTQFRQA 300

Query: 301 AEVLAIESNAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM 360
           AEVLAIE+NAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM
Sbjct: 301 AEVLAIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNMALAIAEIGSLSERRISLM 360

Query: 361 MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420
           MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM
Sbjct: 361 MDKHMSQLPPFLVANGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSM 420

Query: 421 APAAGKRLWEMAENTRGILAVEWLAAVQGLDLRNGLKTSPKLEKARAILRNEVPFYEKDR 480
           APAAGKRLWEMAENTRG+LAVEWLAA QGLDLR GLKTS KLEKARAILR EVPFYEKDR
Sbjct: 421 APAAGKRLWEMAENTRGVLAVEWLAAAQGLDLREGLKTSTKLEKARAILRAEVPFYEKDR 480

Query: 481 FFAPDINAASELLASRCLNELVSAKLLPSL 510
           FFAPDINAASELLA+RCLNELVSAKLLPSL
Sbjct: 481 FFAPDINAASELLATRCLNELVSAKLLPSL 510


Lambda     K      H
   0.317    0.131    0.366 

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: 828
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: 510
Length of database: 510
Length adjustment: 34
Effective length of query: 476
Effective length of database: 476
Effective search space:   226576
Effective search space used:   226576
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate Pf1N1B4_1581 (Histidine ammonia-lyase (EC 4.3.1.3))
to HMM TIGR01225 (hutH: histidine ammonia-lyase (EC 4.3.1.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.16937.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16937.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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