GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Pseudomonas litoralis 2SM5

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_090272720.1 BLU11_RS07260 aldehyde dehydrogenase family protein

Query= BRENDA::P42412
         (487 letters)



>NCBI__GCF_900105005.1:WP_090272720.1
          Length = 483

 Score =  271 bits (692), Expect = 5e-77
 Identities = 161/471 (34%), Positives = 260/471 (55%), Gaps = 5/471 (1%)

Query: 9   NYINGEWVE--SKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVP 66
           +++NG +VE  S+ D  E+      +E++ +   +     + A   A +A  +W +    
Sbjct: 8   SFVNGVFVEADSQCDVLENRNPSNAEEIVDRFARADAALTEKAIAAARDAAGSWGRTNPQ 67

Query: 67  RRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDS 126
            RA IL      + + ++ELA L++ E GK  +EALGEV R   + +F A       G+ 
Sbjct: 68  VRADILDRIGSEILERRQELAELLSREEGKVVREALGEVERAGRSFKFYAQEVLRANGEK 127

Query: 127 LASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTE 186
             S+   V    +  PIGVVG I+P+NFP+ +P W    A+A GNT ++KP+E  P    
Sbjct: 128 YESVREGVSVDVFTQPIGVVGIISPWNFPIAIPAWKAAPALAFGNTVVMKPAELVPSSAW 187

Query: 187 KLVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLK 245
            L E+  ++G+P GVFN+V G    V + I+  P++ AI+F GS+  G  V +  ++ L 
Sbjct: 188 ALAEIISRSGMPAGVFNLVIGPGRTVGDTIIRSPKVDAITFTGSEGTGRQVAEIAAQRLI 247

Query: 246 RVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQ 305
           RVQ   G KN  +VL+DA+L+  +   +  +F S G+RC A + + V  GI DEF+A+L 
Sbjct: 248 RVQLEMGGKNPLVVLDDADLDVAIEVALNGSFYSTGQRCTASSRLIVTTGIHDEFVARLA 307

Query: 306 EKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDG-YFV 364
           E+   +++G+ L     +GPV+     K+ L+YIE GL+EGA L+C G    +D G Y  
Sbjct: 308 ERTRALRVGDPLCADTDIGPVVDPSQLKQNLAYIESGLQEGATLICGGEYLENDKGAYHF 367

Query: 365 GPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRY 424
            P +F +V   M I+++EIF PVLSV++V N +EA++ A  ++++  A + T++     +
Sbjct: 368 SPALFVDVQPHMRIYREEIFGPVLSVLKVANYEEALQAAEDTQYSLSAGIVTTSLKYAEH 427

Query: 425 FRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKK 475
           F+++  AGM+ +NL         PF G + S  G     G  +  F+TR K
Sbjct: 428 FKKHSSAGMVMVNLPTAGVDYHAPFGGNRGSSLGP-REQGTYARQFFTRVK 477


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: 541
Number of extensions: 22
Number of successful extensions: 3
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: 483
Length adjustment: 34
Effective length of query: 453
Effective length of database: 449
Effective search space:   203397
Effective search space used:   203397
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 24 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