GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Tistlia consotensis USBA 355

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_179243903.1 B9O00_RS00790 aldehyde dehydrogenase family protein

Query= BRENDA::P42412
         (487 letters)



>NCBI__GCF_900177295.1:WP_179243903.1
          Length = 480

 Score =  278 bits (710), Expect = 4e-79
 Identities = 172/476 (36%), Positives = 251/476 (52%), Gaps = 8/476 (1%)

Query: 9   NYINGEWVESKTDQYEDVVNPAT-KEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPR 67
           N I GEWV++         NP+   +V+             A   AA AF  WS+    +
Sbjct: 6   NLIAGEWVDAPNASENR--NPSDLSDVVGLYAQGDAAQAGQAIDAAAAAFPAWSRSTPQQ 63

Query: 68  RARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSL 127
           R  IL      +   KEEL  L++ E GK   E +GE  R  +  +F AG    + GD +
Sbjct: 64  RFDILDAAGTEILARKEELGRLLSREEGKTLPEGIGETVRAGQIFKFFAGEALRIAGDRI 123

Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187
            S    V A   R P+GVVG I P+NFP+ +P W    A+A GN  ++KP++  P     
Sbjct: 124 DSTRPGVIAEATREPLGVVGLITPWNFPIAIPAWKLAPALAFGNCVVMKPADLVPGCAWA 183

Query: 188 LVELFEKAGLPKGVFNVVYGAHDVV-NGILEHPEIKAISFVGSKPVGEYVYKK--GSENL 244
           L ++ ++AGLPKGVFN+V G   VV   IL  P++ AISF GS   G +V ++    E +
Sbjct: 184 LADILQRAGLPKGVFNLVMGRGSVVGEAILASPKVAAISFTGSVATGRHVARRCIEGEAM 243

Query: 245 KRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKL 304
           K+ Q   G KN  +VL+DA+LE    + +  AF S G+RC A + + V EGI D F+  L
Sbjct: 244 KKFQLEMGGKNPFVVLDDADLEVAANSALNGAFFSTGQRCTASSRLIVTEGIHDRFVEAL 303

Query: 305 QEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDG-RENVSDDGYF 363
             K+  +K+ N L +G  +GPV+ +    + L YI+ G +EGA+L   G R N   +G++
Sbjct: 304 TSKLKALKVDNALKEGTQIGPVVDQRQLDQDLDYIKVGQDEGAKLAWGGERLNRETEGFY 363

Query: 364 VGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIR 423
           + P +F      M I ++EIF PV SVIRVK+   A+ +AN ++F   A + TS+     
Sbjct: 364 LQPALFTETDNAMRINREEIFGPVASVIRVKDYDSALAVANDTQFGLSAGIATSSLKHAE 423

Query: 424 YFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTA 479
           +F+ N  AGM+ +NL         PF G K+S +G     G+ +V+FYT  K   A
Sbjct: 424 HFKRNSQAGMVMVNLPTAGVDYHVPFGGRKNSSYGA-REQGRYAVEFYTTVKTAYA 478


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: 515
Number of extensions: 30
Number of successful extensions: 5
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: 480
Length adjustment: 34
Effective length of query: 453
Effective length of database: 446
Effective search space:   202038
Effective search space used:   202038
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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