GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Microvirga lotononidis WSM3557

Align Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Matured fruit 60 kDa protein; MF-60; EC 1.2.1.3 (characterized)
to candidate WP_009763131.1 MICLODRAFT_RS17515 aldehyde dehydrogenase family protein

Query= SwissProt::Q9ZPB7
         (508 letters)



>NCBI__GCF_000262405.1:WP_009763131.1
          Length = 516

 Score =  482 bits (1241), Expect = e-140
 Identities = 241/472 (51%), Positives = 325/472 (68%), Gaps = 3/472 (0%)

Query: 39  VSPSNNQEIAKVTEVSMEEYEEGLRSCNDAAKTWKSLPAPKRGEIVRQIGDALREKLQHL 98
           +SP   + IA V E + +E +  +   + A K W+ +PAPKRGE +R +G+ LR     L
Sbjct: 41  LSPITGEVIAHVRETTPDEAKAAIGRADAAFKAWRKVPAPKRGEFIRLLGEELRAAKDDL 100

Query: 99  GKLVSLEMGKILAEGIGEVQEVIYMCDFAVGLSRQLNGSIIPSERPDHMMFEVWNPLGIV 158
           G+LV+LE GKI++EG+GEVQE+I +CDFAVGLSRQL G  I +ER DH M E W+PLG+ 
Sbjct: 101 GRLVTLEAGKIVSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERADHRMMETWHPLGVC 160

Query: 159 GVITAFNFPCAVLGWNACIALVCGNCVVWKGAPTTPLVTIAVTKLIAEVLEK-NNLPAAI 217
           GVI+AFNFP AV  WNA +ALVCG+ VVWK +  T L  +A   ++    ++   +P  +
Sbjct: 161 GVISAFNFPVAVWSWNAALALVCGDSVVWKPSEKTLLTALATHAIVERAAKRFGGVPEGL 220

Query: 218 FTAFCGGAEIGEAIAKDTRIPLVSFTGSSKVGAKVQQIVTERFGKCLLELSGNNALIVMD 277
                GG EIGE + +D R+P++S TGS+ +G +V   + ERF + +LEL GNNA IV  
Sbjct: 221 CEVLLGGREIGEILVEDHRVPVLSATGSTAMGRQVGPKLAERFARAILELGGNNAAIVAP 280

Query: 278 DADVGLAVRSIFFAAVGTAGQRCTTCRRLYLHESIYQNVLDKLVGLYNQVKIGDPLEEGT 337
            AD+ LA+R I FAA+GTAGQRCTT RRL++HES+Y  ++ +LV +Y  VKIGDP  EGT
Sbjct: 281 SADLDLALRGIAFAAMGTAGQRCTTLRRLFVHESVYDQLVPRLVKVYGSVKIGDPRAEGT 340

Query: 338 LVGPVHTKASRENFEKGISTIKSQGGKILTGG--SVIESDGNFVQPTIVEIASNASVVKE 395
           LVGP+  KA+ +N E+ +   ++ GGK+  GG  + + ++G + +P +VE+ S    V  
Sbjct: 341 LVGPLIDKAAFDNMERALDEARAAGGKVHGGGRYTDVANEGVYARPALVEMPSQTGPVTR 400

Query: 396 ELFGPVLYVMKFKTLEEAIALNNSVPQGLSSSIFTSKPNTIFKWIGPHGSDCGIVNVNIP 455
           E F P+LYVM++   +E IAL+N+V  GLSSSIFT        ++   GSDCGI NVNI 
Sbjct: 401 ETFAPILYVMRYSDFDEVIALHNAVGAGLSSSIFTLNLREAEAFVSAAGSDCGIANVNIG 460

Query: 456 TNGAEIGGAFGGEKATGGGREAGSDSWKQYMRRSTCTINYGTELPLAQGINF 507
            +GAEIGGAFGGEK TGGGRE+GSD+WK YMRR+T TINYG+ LPLAQG+ F
Sbjct: 461 PSGAEIGGAFGGEKETGGGRESGSDAWKAYMRRATNTINYGSTLPLAQGVKF 512


Lambda     K      H
   0.317    0.136    0.404 

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: 708
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: 508
Length of database: 516
Length adjustment: 35
Effective length of query: 473
Effective length of database: 481
Effective search space:   227513
Effective search space used:   227513
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 Sep 24 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