GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_2 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2
          Length = 497

 Score =  902 bits (2331), Expect = 0.0
 Identities = 441/496 (88%), Positives = 465/496 (93%)

Query: 1   MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60
           M++I HLI GEL+ + GR  DVFNPSTG+A+ K+PLA RET+Q AIDAAKAAFPAWRNTP
Sbjct: 1   MSVIPHLINGELVTENGRAVDVFNPSTGQAIHKLPLATRETIQSAIDAAKAAFPAWRNTP 60

Query: 61  PAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKG 120
           PAKRAQV+FRFKQLLE NE RI +LISEEHGKT+EDAAGELKRGIENVE+A AAPEILKG
Sbjct: 61  PAKRAQVMFRFKQLLEQNEARIAQLISEEHGKTLEDAAGELKRGIENVEFACAAPEILKG 120

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

Query: 181 TLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240
           TLLIA+L  EAGLPKGVL+VVHGDK AVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG
Sbjct: 181 TLLIAQLLLEAGLPKGVLSVVHGDKTAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240

Query: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQK 300
           KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVG+Q+ADALV K
Sbjct: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGEQVADALVAK 300

Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360
           LVPQIK LKIGAGT+CGLDMGPLVTG ARDKV+GY++ GVA GA LVVDGRG  VAGHE 
Sbjct: 301 LVPQIKALKIGAGTNCGLDMGPLVTGQARDKVSGYVEDGVAAGATLVVDGRGLTVAGHEE 360

Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420
           GFFLGG LFD VTPEM IYKEEIFGPVLC+VRVNSLEEAMQLINDHEYGNGTCIFTRDGE
Sbjct: 361 GFFLGGCLFDNVTPEMRIYKEEIFGPVLCVVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420

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

Query: 481 WPQRKSHEAAQFAFPS 496
           WPQR SHEA+QFAFPS
Sbjct: 481 WPQRASHEASQFAFPS 496


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: 904
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: 498
Length of database: 497
Length adjustment: 34
Effective length of query: 464
Effective length of database: 463
Effective search space:   214832
Effective search space used:   214832
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 PfGW456L13_2 (Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27))
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.30328.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30328.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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