GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Burkholderia phytofirmans PsJN

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate BPHYT_RS28030 BPHYT_RS28030 methylmalonate-semialdehyde dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_5146
         (508 letters)



>FitnessBrowser__BFirm:BPHYT_RS28030
          Length = 503

 Score =  847 bits (2188), Expect = 0.0
 Identities = 418/500 (83%), Positives = 457/500 (91%)

Query: 9   DTTVQKVKLLIDGQWVESKTTEWHDIINPATQQVLAKVPFATAEEVDAAISAAHRAFQTW 68
           +  V  VKLLI+G++VESKTTEW DI+NPATQ+VLA+VPFATA+EV+ AI +AH AF+TW
Sbjct: 4   NAAVATVKLLINGEFVESKTTEWRDIVNPATQEVLARVPFATADEVNEAIRSAHAAFKTW 63

Query: 69  KLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVVEHACSIGS 128
           K TPIGARMRIMLK QALIREHS RIA  LSAEQGKTI DAEGDIFRGLEVVEHACSIG+
Sbjct: 64  KDTPIGARMRIMLKYQALIREHSPRIARTLSAEQGKTIPDAEGDIFRGLEVVEHACSIGT 123

Query: 129 LQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQ 188
           LQ GEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAI CGNTFVLKPSEQ
Sbjct: 124 LQQGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIVCGNTFVLKPSEQ 183

Query: 189 DPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDGLCTHKDIKAVSFVGSTAVGTHVYDLA 248
           DP+STM LVELA+EAG+P GVLNVVHGGK+VVD LCTH+ +KAVSFVGSTAVGTHVY L 
Sbjct: 184 DPLSTMQLVELALEAGVPKGVLNVVHGGKEVVDALCTHELVKAVSFVGSTAVGTHVYRLG 243

Query: 249 GKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGAAKQWL 308
            +HGKRVQSMMGAKNHAVVLPDANREQ LNAL GAGFGAAGQRCMATSVVVLVGAA+QWL
Sbjct: 244 SEHGKRVQSMMGAKNHAVVLPDANREQTLNALAGAGFGAAGQRCMATSVVVLVGAAQQWL 303

Query: 309 PDLKALAQKLKVNAGSEPGTDVGPVISKKAKARILDLIESGIKEGAKLELDGREISVPGY 368
           PDL A A+ LKVNAG+EP TD+GPV+S+ AK RIL LIE+G+KEGA L LDGR+I VPGY
Sbjct: 304 PDLVAKARTLKVNAGNEPNTDIGPVVSRAAKQRILGLIEAGVKEGATLALDGRDIKVPGY 363

Query: 369 EKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVNTLDEAIALVNANPFGNGTGLFTQS 428
           E+GNF+GPT+FS VTT+M+IY QEIFGPVLVVL   TLD+AIALVN NPFGNG GLFTQS
Sbjct: 364 EQGNFIGPTVFSDVTTEMEIYRQEIFGPVLVVLNAATLDDAIALVNRNPFGNGVGLFTQS 423

Query: 429 GAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVT 488
           GAAARKFQ+EID+GQVGINIPIPVPVP FSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVT
Sbjct: 424 GAAARKFQSEIDIGQVGINIPIPVPVPSFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVT 483

Query: 489 SRWFDDDSVNDGVNTTINLR 508
           +RWFDDD+VNDGVNTTI+LR
Sbjct: 484 ARWFDDDTVNDGVNTTISLR 503


Lambda     K      H
   0.318    0.135    0.395 

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: 842
Number of extensions: 28
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: 508
Length of database: 503
Length adjustment: 34
Effective length of query: 474
Effective length of database: 469
Effective search space:   222306
Effective search space used:   222306
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 BPHYT_RS28030 BPHYT_RS28030 (methylmalonate-semialdehyde dehydrogenase)
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.27369.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27369.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.