GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutH in Pseudomonas fluorescens FW300-N2E3

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate AO353_17725 AO353_17725 histidine ammonia-lyase

Query= reanno::pseudo1_N1B4:Pf1N1B4_1582
         (507 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_17725
          Length = 512

 Score =  903 bits (2333), Expect = 0.0
 Identities = 463/512 (90%), Positives = 484/512 (94%), Gaps = 5/512 (0%)

Query: 1   MSQAEKIVIADAPLRWQDVVAVARHGAQLELSPQIWTRIENAQAIVQRIVASGERAYGVN 60
           MSQA+KIVIADAPLRWQDVVAVARHGA LELS Q W RI+NAQAIVQ IV SGERAYGVN
Sbjct: 1   MSQAKKIVIADAPLRWQDVVAVARHGAVLELSAQTWARIDNAQAIVQHIVVSGERAYGVN 60

Query: 61  TGLGALCNVSLKGEQLSQLSRNTLLSHACGVGAPLADEQTRAIICAAIRNYSHGKSGIHR 120
           TGLGALCNVSL+GEQLSQLSRNTLLSHACGVGAPL DEQTR+I+CAAI NYSHGKSG+HR
Sbjct: 61  TGLGALCNVSLQGEQLSQLSRNTLLSHACGVGAPLTDEQTRSIMCAAIINYSHGKSGLHR 120

Query: 121 RVVEALLALLNRGITPQVPSQGSVGYLTHMAHIGITLLGVGNVSYRGQIVTAQQALSEEG 180
           +VVEALLALLNRGITPQVPSQGSVGYLTHMAHIGI+LLGVG VSYRGQIV AQQAL+EEG
Sbjct: 121 QVVEALLALLNRGITPQVPSQGSVGYLTHMAHIGISLLGVGQVSYRGQIVPAQQALAEEG 180

Query: 181 LQPVQLGAKDGLCLVNGTPCMTGLSCLAIADATRLVQWADVIGAMSFEAQRGQIAAFDAE 240
           L+PVQLGAKDGLCLVNGTPCMTGLSCLA+ADATRL+QWADVIGAMSFEAQRGQI AFDAE
Sbjct: 181 LKPVQLGAKDGLCLVNGTPCMTGLSCLALADATRLIQWADVIGAMSFEAQRGQIDAFDAE 240

Query: 241 IIALKPHLGMQQVGINLRALLDGSEVIASSKGIRTQDALSIRSIPQVHGAARDQLEHAKK 300
           IIALKPH GMQQVGINLR LLDGSEVIASSKGIRTQDALSIRSIPQVHGAARDQL+HA +
Sbjct: 241 IIALKPHPGMQQVGINLRGLLDGSEVIASSKGIRTQDALSIRSIPQVHGAARDQLDHATR 300

Query: 301 QIETELNSVTDNPMLLGTPDNFRVMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRL 360
           QIETELNS TDNP+LLGTPDN+RVMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRL
Sbjct: 301 QIETELNSATDNPLLLGTPDNYRVMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRL 360

Query: 361 INPHVSGLPAFLVANPGVNSGMMIVQYVAASLCAENRQLAQPAVLDNYVTSGLQEDHLSM 420
           INPHVSGLPAFLV+NPGVNSGMMIVQYVAASLCAENRQLAQPAVLDNYVTSGLQEDHLSM
Sbjct: 361 INPHVSGLPAFLVSNPGVNSGMMIVQYVAASLCAENRQLAQPAVLDNYVTSGLQEDHLSM 420

Query: 421 GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKEQ-----RFGAGTDTAWRLLRERVPA 475
           GTNAALKLHRALENCTQILAIEYLLAAQAFEFLK        FGAGT+ AWRLLRERVPA
Sbjct: 421 GTNAALKLHRALENCTQILAIEYLLAAQAFEFLKADFLKGPCFGAGTEVAWRLLRERVPA 480

Query: 476 YDQDRWLAPDIAAAAGVLKDPILLHKALPNLN 507
           YDQDRWLAPDIA+AA VLKDP LL  ALP+L+
Sbjct: 481 YDQDRWLAPDIASAASVLKDPQLLQTALPSLH 512


Lambda     K      H
   0.319    0.133    0.384 

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: 976
Number of extensions: 24
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: 507
Length of database: 512
Length adjustment: 34
Effective length of query: 473
Effective length of database: 478
Effective search space:   226094
Effective search space used:   226094
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate AO353_17725 AO353_17725 (histidine ammonia-lyase)
to HMM TIGR01225 (hutH: histidine ammonia-lyase (EC 4.3.1.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.13347.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13347.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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