GapMind for catabolism of small carbon sources

 

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

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_011383730.1 AMB_RS06710 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>NCBI__GCF_000009985.1:WP_011383730.1
          Length = 485

 Score =  348 bits (892), Expect = e-100
 Identities = 188/465 (40%), Positives = 279/465 (60%), Gaps = 2/465 (0%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           YI+G +V  +    + V NPA  ++I R+P   A + R+AI+AA+RA   W+A  A ER+
Sbjct: 15  YINGSWVAAQSGERLAVTNPADGSLIIRVPAMGAAETRQAIEAADRAWGPWKAKTAKERS 74

Query: 70  SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129
           + LR+    I    ++++ L+  E GK    A+ EVA+ A ++++ AE A+R  G+ I  
Sbjct: 75  AVLRRWFELIMAAQNDLAKLMTAEQGKPLAEAKGEVAYGASFVEWFAEEAKRVYGDTIPE 134

Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189
             PG  I++ K  +GV   I PWNFP  +I RK APAL  G  +V+KP+E TP +A+A A
Sbjct: 135 HMPGRRIVVVKEPIGVVAAITPWNFPLAMITRKCAPALAAGCPVVVKPAEDTPLSALALA 194

Query: 190 KIVDEIGLPRGVFNLV-LGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248
           ++ +  G P GVFN++  G  + VG EL  NPKV  +S TGS   G+ +MA  A  + K+
Sbjct: 195 ELAERAGFPPGVFNVITAGDPKAVGFELTANPKVRKLSFTGSTEVGKLLMAQCAATVKKL 254

Query: 249 CLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEA 308
            LELGG AP +V DDADL+ AV   + S+  N+GQ C CA R+ VQ GIYD F  RL EA
Sbjct: 255 SLELGGNAPFMVFDDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDGIYDAFTARLAEA 314

Query: 309 MQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPT 368
           + A++ G P    D   GPLIN  A+ +VE+ +A AV +GARV  GGK     G ++ PT
Sbjct: 315 VAALKVG-PGLEGDFQQGPLINEEAVRKVERHIADAVAKGARVVMGGKRHARGGTFFEPT 373

Query: 369 LLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIK 428
           +L DV  +M+   EETFGPV P+  F T E+A+ MAND+++GL +  Y++++    +  +
Sbjct: 374 ILADVTPDMAPAREETFGPVAPLFRFKTEEEAVRMANDTEFGLAAYFYSRDVGRVWRVSR 433

Query: 429 GLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQ 473
            L++G   IN            G ++SG+G    K+G+ ++L+ +
Sbjct: 434 ALEYGIVGINEGLISTEVAPFGGVKESGLGREGSKYGIEDFLEVK 478


Lambda     K      H
   0.318    0.135    0.392 

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: 543
Number of extensions: 27
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: 479
Length of database: 485
Length adjustment: 34
Effective length of query: 445
Effective length of database: 451
Effective search space:   200695
Effective search space used:   200695
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