GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Pseudomonas simiae WCS417

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF640 PS417_03250 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__WCS417:GFF640
          Length = 498

 Score =  911 bits (2354), Expect = 0.0
 Identities = 445/498 (89%), Positives = 471/498 (94%)

Query: 1   MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60
           M+LI+HLI GEL+ D+GR+ADV+NPSTG+ + +VPLA RET+QQAID+AKAAFPAWRNTP
Sbjct: 1   MSLIQHLINGELVNDSGRSADVYNPSTGQVIHQVPLASRETIQQAIDSAKAAFPAWRNTP 60

Query: 61  PAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKG 120
            AKRAQV+FRFKQLLE NE RI +LISEEHGKT+EDAAGELKRGIENVEYA +APEILKG
Sbjct: 61  AAKRAQVMFRFKQLLEQNEARISQLISEEHGKTLEDAAGELKRGIENVEYACSAPEILKG 120

Query: 121 EYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSS 180
           EYSRNVGPNIDAWSDFQP+GVVAGITPFNFPAMVPLWMYPLAI CGN FILKPSERDPSS
Sbjct: 121 EYSRNVGPNIDAWSDFQPLGVVAGITPFNFPAMVPLWMYPLAIVCGNCFILKPSERDPSS 180

Query: 181 TLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240
           TLLIA+L  EAGLPKGVL+VVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSE TKRG
Sbjct: 181 TLLIAQLLQEAGLPKGVLSVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEATKRG 240

Query: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQK 300
           KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQ+ADAL+ K
Sbjct: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQVADALIAK 300

Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360
           LVPQ+K LKIGAGTSCGLDMGPLVTG ARDKV+GYID GVA GAELVVDGRG  VAGHE 
Sbjct: 301 LVPQVKALKIGAGTSCGLDMGPLVTGQARDKVSGYIDDGVAAGAELVVDGRGLSVAGHEE 360

Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420
           GFFLGG+LFDRVTPEM IYKEEIFGPVLC+VRVNSLE AMQLINDHEYGNGTCIFTRDGE
Sbjct: 361 GFFLGGSLFDRVTPEMRIYKEEIFGPVLCVVRVNSLEAAMQLINDHEYGNGTCIFTRDGE 420

Query: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQR 480
           AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYT+RKAITQR
Sbjct: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTRRKAITQR 480

Query: 481 WPQRKSHEAAQFAFPSNS 498
           WPQR SHEA+QFAFPS S
Sbjct: 481 WPQRASHEASQFAFPSLS 498


Lambda     K      H
   0.319    0.137    0.411 

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: 918
Number of extensions: 18
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: 498
Length of database: 498
Length adjustment: 34
Effective length of query: 464
Effective length of database: 464
Effective search space:   215296
Effective search space used:   215296
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate GFF640 PS417_03250 (methylmalonate-semialdehyde dehydrogenase)
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.11121.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11121.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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