GapMind for catabolism of small carbon sources

 

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

Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate Pf1N1B4_1107 D-galactarate dehydratase (EC 4.2.1.42)

Query= reanno::WCS417:GFF829
         (517 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1107
          Length = 517

 Score = 1003 bits (2593), Expect = 0.0
 Identities = 498/517 (96%), Positives = 509/517 (98%)

Query: 1   MQLIEHADSPRSIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDFIPQSHKVTLEDIPEG 60
           MQLIEH+DSPR IRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDF+PQSHKVTLEDIPEG
Sbjct: 1   MQLIEHSDSPRYIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDFVPQSHKVTLEDIPEG 60

Query: 61  GQIIRYGQTIGYALAPIPRGSWVQEDQLRMPTAPPLDSLPLSTEVPEAQAPLEGFTFEGY 120
           GQ+IRYGQTIGYAL PIPRGSWV+EDQLRMPTAPPLDSLPLSTEVP AQAPLEGFTFEGY
Sbjct: 61  GQVIRYGQTIGYALQPIPRGSWVKEDQLRMPTAPPLDSLPLSTEVPAAQAPLEGFTFEGY 120

Query: 121 RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAI 180
           RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYP+VDDVVALTHSYGCGVAI
Sbjct: 121 RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPNVDDVVALTHSYGCGVAI 180

Query: 181 TATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHDNDSSVDLSEPWLYRLQD 240
           TATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMH+NDSSVDLS+PWLYRLQD
Sbjct: 181 TATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHENDSSVDLSDPWLYRLQD 240

Query: 241 SSHGFTEMIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA 300
           SSHGFTEMIEQIMALAETRLKKLD RRRETVPASELILGMQCGGSDAFSGITANPALGYA
Sbjct: 241 SSHGFTEMIEQIMALAETRLKKLDLRRRETVPASELILGMQCGGSDAFSGITANPALGYA 300

Query: 301 SDLLLRAGATVMFSEVTEVRDAIYLLTSRAENTQVAQELVREMDWYDRYLAKGEADRSAN 360
           SDLLLRAGATVMFSEVTEVRDAIYLLTSRAE  +VAQELVREMDWYDRYLAKGEADRSAN
Sbjct: 301 SDLLLRAGATVMFSEVTEVRDAIYLLTSRAETEEVAQELVREMDWYDRYLAKGEADRSAN 360

Query: 361 TTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFKGKGLIFCATPASDFVCGTLQ 420
           TTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFK KGLIFCATPASDFVCGTLQ
Sbjct: 361 TTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFKRKGLIFCATPASDFVCGTLQ 420

Query: 421 LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRATIEELG 480
           LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRA+IEELG
Sbjct: 421 LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRASIEELG 480

Query: 481 WELFHFYLDVASGRKQTWAEHHKLHNDITLFNPAPIT 517
           WELFH+YLDVASG+KQTWAE HKLHNDITLFNPAPIT
Sbjct: 481 WELFHYYLDVASGKKQTWAEQHKLHNDITLFNPAPIT 517


Lambda     K      H
   0.318    0.135    0.401 

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: 986
Number of extensions: 17
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: 517
Length of database: 517
Length adjustment: 35
Effective length of query: 482
Effective length of database: 482
Effective search space:   232324
Effective search space used:   232324
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_1107 (D-galactarate dehydratase (EC 4.2.1.42))
to HMM TIGR03248 (garD: galactarate dehydratase (EC 4.2.1.42))

Software error:

../bin/blast/fastacmd -i /tmp/list.29691.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29691.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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