GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Magnetospirillum magneticum AMB-1

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011383730.1 AMB_RS06710 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P42412
         (487 letters)



>NCBI__GCF_000009985.1:WP_011383730.1
          Length = 485

 Score =  231 bits (589), Expect = 4e-65
 Identities = 141/451 (31%), Positives = 232/451 (51%), Gaps = 4/451 (0%)

Query: 10  YINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRRA 69
           YING WV +++ +   V NPA   ++ +VP     +   A + A  A+  W       R+
Sbjct: 15  YINGSWVAAQSGERLAVTNPADGSLIIRVPAMGAAETRQAIEAADRAWGPWKAKTAKERS 74

Query: 70  RILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLAS 129
            +L  + +L+   + +LA L+T E GK   EA GEV  G   VE+ A     + GD++  
Sbjct: 75  AVLRRWFELIMAAQNDLAKLMTAEQGKPLAEAKGEVAYGASFVEWFAEEAKRVYGDTIPE 134

Query: 130 IATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKLV 189
                     + PIGVV  I P+NFP+ +       A+A G   ++KP+E TPL    L 
Sbjct: 135 HMPGRRIVVVKEPIGVVAAITPWNFPLAMITRKCAPALAAGCPVVVKPAEDTPLSALALA 194

Query: 190 ELFEKAGLPKGVFNVVYGAHDVVNG--ILEHPEIKAISFVGSKPVGEYVYKKGSENLKRV 247
           EL E+AG P GVFNV+        G  +  +P+++ +SF GS  VG+ +  + +  +K++
Sbjct: 195 ELAERAGFPPGVFNVITAGDPKAVGFELTANPKVRKLSFTGSTEVGKLLMAQCAATVKKL 254

Query: 248 QSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEK 307
               G     +V +DA+L+  V   + + + + G+ C+    + V++GI D F A+L E 
Sbjct: 255 SLELGGNAPFMVFDDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDGIYDAFTARLAEA 314

Query: 308 VADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVGPT 367
           VA +K+G GL+     GP+I E+  ++   +I   + +GAR+V  G+ + +  G F  PT
Sbjct: 315 VAALKVGPGLEGDFQQGPLINEEAVRKVERHIADAVAKGARVVMGGKRH-ARGGTFFEPT 373

Query: 368 IFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFRE 427
           I  +VT +M   ++E F PV  + R K  +EA+ +AN +EF   A  ++ +   +     
Sbjct: 374 ILADVTPDMAPAREETFGPVAPLFRFKTEEEAVRMANDTEFGLAAYFYSRDVGRVWRVSR 433

Query: 428 NIDAGMLGINLGVPAPMAFFPFSGWKSSFFG 458
            ++ G++GIN G+       PF G K S  G
Sbjct: 434 ALEYGIVGINEGL-ISTEVAPFGGVKESGLG 463


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: 532
Number of extensions: 24
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: 485
Length adjustment: 34
Effective length of query: 453
Effective length of database: 451
Effective search space:   204303
Effective search space used:   204303
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