GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Magnetospirillum magneticum AMB-1

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>lcl|NCBI__GCF_000009985.1:WP_011383257.1 AMB_RS04160 NAD-dependent
           succinate-semialdehyde dehydrogenase
          Length = 499

 Score =  545 bits (1404), Expect = e-159
 Identities = 267/485 (55%), Positives = 361/485 (74%), Gaps = 5/485 (1%)

Query: 41  DLHADLLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFS 98
           DL   L++  ++V G W+       F V DPA+G  + +V D G  E R A+ AA  A++
Sbjct: 17  DLDPSLIKSHAYVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAEAAWN 76

Query: 99  SWKEISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEE 158
            W++ + K+R++++  W+DL++ ++D LA++++AE GKPL EA GEI Y A F+ WF+EE
Sbjct: 77  PWRQRTAKDRAAVMMAWHDLIMAHQDALARLLSAEQGKPLAEAMGEISYGASFISWFAEE 136

Query: 159 ARRVYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPA 218
            +R YGD+I T+A D+R LV+KQP+GV + +TPWNFP AMITRK   ALAAGC VVVKPA
Sbjct: 137 GKRAYGDLIPTTASDRRLLVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPA 196

Query: 219 EDTPYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGK 278
           EDTP SALALA+LA++AG+P G++N++   +  A  VG  +  +  V K+SFTGST  GK
Sbjct: 197 EDTPLSALALAELAHRAGLPKGLFNIVTTRQPAA--VGGEMTGNAKVRKLSFTGSTRVGK 254

Query: 279 ILLHHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQR 338
           +L+   A +VK+VS+ELGG APFIVFD  ++D AVAGA+ASK+RN+GQTC+C+NRFLVQ 
Sbjct: 255 LLMAQCAETVKKVSLELGGNAPFIVFDDCDLDAAVAGALASKYRNSGQTCICTNRFLVQA 314

Query: 339 GIHDSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGG 398
           GI++ F  K AE    ++ VG+       QGPLIN  AV KV  HV DAV+KGA V+TGG
Sbjct: 315 GIYEDFAVKLAEKAA-AMAVGHALSGVVQQGPLINAAAVAKVAAHVADAVSKGARVLTGG 373

Query: 399 KRHQSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYF 458
           + H  GG F++PT+L++VT  MLC  EETFGPVAP+++F+ E EA+A+ANA++ GLAGYF
Sbjct: 374 RPHALGGGFWQPTVLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGYF 433

Query: 459 YSQDPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYV 518
           YS+D A+++RVAE LE GMVGVNE LIS+   PFGG+K+SGLGREGSKYG+D+++E KYV
Sbjct: 434 YSRDVARVFRVAEALECGMVGVNESLISNEVAPFGGIKESGLGREGSKYGLDDFMETKYV 493

Query: 519 CYGGL 523
           C GGL
Sbjct: 494 CIGGL 498


Lambda     K      H
   0.318    0.135    0.400 

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: 665
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: 523
Length of database: 499
Length adjustment: 35
Effective length of query: 488
Effective length of database: 464
Effective search space:   226432
Effective search space used:   226432
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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