GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Azospirillum brasilense Sp245

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate AZOBR_RS29750 AZOBR_RS29750 aldehyde dehydrogenase

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__azobra:AZOBR_RS29750
          Length = 484

 Score =  271 bits (692), Expect = 5e-77
 Identities = 162/473 (34%), Positives = 251/473 (53%), Gaps = 10/473 (2%)

Query: 6   KLKNYINGEWVESKTDQYEDVVNPATKEVLC-QVPISTKEDIDYAAQTAAEAFKTWSKVA 64
           ++ N+I G W   +  +  D+VNP+  + L     ++  +D+  A   A  A   W    
Sbjct: 7   RITNFIAGSWRPGR--ERLDIVNPSNLDELAGSYSLAGADDVAEAVAAARAAQPQWRAAT 64

Query: 65  VPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMG 124
           V +R+ +L    + L   K+ELA +   E GK   +ALGE+ R      F A       G
Sbjct: 65  VEQRSLVLDAISRALFDRKDELARIAATEGGKTIPDALGEITRAAHLARFFAAEALRAPG 124

Query: 125 DSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTP-- 182
           ++L S+   VE    R P+GV+G + P+NFP+  P W    A+A GN  I KPSE+TP  
Sbjct: 125 ETLGSVRPGVEVDVTREPVGVIGLVTPWNFPVATPMWKIAPALAFGNAVIWKPSEKTPGI 184

Query: 183 --LLTEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKG 240
              +T  + E  E  G+P  +FN+V GA   + G      + A+SF GS   G  +  + 
Sbjct: 185 SIAVTRLIAEALEAHGMPAALFNLVIGAGPNI-GAAVVDAVDAVSFTGSVNTGRRIAVRC 243

Query: 241 SENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEF 300
           +E + RVQ   G +N  +VL DA+ E      V +A+  AG+RC A     VE+ I D F
Sbjct: 244 AERMIRVQLELGGQNPLVVLGDADPERAAEIGVNSAYFHAGQRCTATGRFIVEDSIHDAF 303

Query: 301 MAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVC-DGRENVSD 359
           +A + E++A +++G+ L     +GPVI E    + L YI+ GL+EGA+L    GR +   
Sbjct: 304 VAAMTERMAALRVGHALLPETQIGPVIDEFQLTKNLHYIDTGLKEGAQLASGGGRLDRPT 363

Query: 360 DGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNS 419
            G+F+ PT+F   +  MTI ++E+F PV SVIRVK+ +EA+ +AN +++   + + T++ 
Sbjct: 364 RGWFLAPTLFTETSNAMTINREEVFGPVASVIRVKDYEEALHVANDTDYGLSSGIITNSM 423

Query: 420 NAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYT 472
              R+F+ NI AGM  +NL         PF G K S +G     G+ +++FYT
Sbjct: 424 KHARHFQANIQAGMTMLNLPTAGVDYHVPFGGRKMSSYGP-REQGRSAIEFYT 475


Lambda     K      H
   0.318    0.136    0.396 

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: 530
Number of extensions: 18
Number of successful extensions: 4
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: 487
Length of database: 484
Length adjustment: 34
Effective length of query: 453
Effective length of database: 450
Effective search space:   203850
Effective search space used:   203850
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)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory