GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Sedimenticola selenatireducens DSM 17993

Align malonate semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.18) (characterized)
to candidate WP_029133426.1 A3GO_RS0110905 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-18958
         (541 letters)



>NCBI__GCF_000428045.1:WP_029133426.1
          Length = 470

 Score =  199 bits (506), Expect = 2e-55
 Identities = 143/461 (31%), Positives = 216/461 (46%), Gaps = 15/461 (3%)

Query: 57  FDIHDPATNNVVSKVPQSTPEELEDAIASAHKAFPKWRDTSIIKRQGIAFKFVQLLRENM 116
           FD+ +PAT  VV+  P ++  +L+ A+A+A +AF +W+ +S   R+ +       +  + 
Sbjct: 21  FDVLNPATEAVVAACPTASVGQLDAAVAAAGEAFRQWQFSSNDTRKQLLHDIADKIEAHA 80

Query: 117 DRIASVIVLEQGKTFADAQGDVLRGLQVAEAACNVTNDLKGESLEVATDMETKMIREPLG 176
             +A ++V EQGK    AQ +V  G  VA        D+  E +E +     +M R+PLG
Sbjct: 81  AELAEIVVAEQGKPMFLAQAEV--GGAVAWTRATAELDIPVEVIEDSPGKRIEMHRKPLG 138

Query: 177 VIGSICPFNFPAMVPLWSLPLVLVTGNTAVVKPSERVPGAAMIICELAAKAGVPAGVLNI 236
           V+GSI P+N+P M+ +W +   L TGNT V+KPSE  P   + + EL  +   P GV+N+
Sbjct: 139 VVGSITPWNWPLMIAVWHIMPALRTGNTVVIKPSEFTPLNTLRLVELINEV-APKGVVNV 197

Query: 237 VHGKHDTVNKLIDDPRIKALTFVGGDKAGKYIYERGSQLGKRVQANLGAKNHLVVLPDAN 296
           V G  D    +    RI  + F G    GK I    +   KR+   LG  +  +VLP  +
Sbjct: 198 VTGMSDIGRAMSVHTRINKIVFTGSTATGKDIMFHAANNLKRLTLELGGNDAGIVLPGTD 257

Query: 297 KQSFVNAVNGAAFGAAGQRCMAISVLVTVGKTTKEWVKDVVADAKLLKTGSGFDPKSDLG 356
             +    +   AF   GQ C A+  L       +     +   A+  + GSG D     G
Sbjct: 258 VDAVAMPIFQGAFLNMGQTCAALKRLYVHDSIYEAMCGKLTEIAQQQQLGSGMDEGVTFG 317

Query: 357 PVINPESLTRAEEIIEDSVQNGAVLELDGRGYKPTNDPEQKFTKGNFLAPTILTNVKPGM 416
           PV N + L    +++ED+  NGA +   G         E+    G F  PTI+     GM
Sbjct: 318 PVQNKKQLQIVSDLVEDARNNGARILCGG---------ERLAGSGYFYPPTIVAEASDGM 368

Query: 417 RAYDEEIFAPVLAVVNVDTIDEAIELINSNKYGNGVSLFTNSGGSAQYFTKRIDVGQVGI 476
           R  DEE F PVL V+    +D+A+   N    G G S++     SA     R++ G   I
Sbjct: 369 RIVDEEQFGPVLPVIRYSDVDDAVRRANDCDAGLGGSVWGADVESATQVATRLECGTAWI 428

Query: 477 NVPIPVPLPMFSFTGSRGSFLGDLNFYGKAGITFLTKPKTI 517
           N    V LP   F G + S  G    +G  G+   T P+ +
Sbjct: 429 NGHAEV-LPHAPFGGCKMSGFG--VEFGVEGLLEYTSPQLL 466


Lambda     K      H
   0.315    0.133    0.383 

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: 566
Number of extensions: 28
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: 541
Length of database: 470
Length adjustment: 34
Effective length of query: 507
Effective length of database: 436
Effective search space:   221052
Effective search space used:   221052
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 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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