GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Cupriavidus basilensis 4G11

Align Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Matured fruit 60 kDa protein; MF-60; EC 1.2.1.3 (characterized)
to candidate RR42_RS18500 RR42_RS18500 aldehyde dehydrogenase

Query= SwissProt::Q9ZPB7
         (508 letters)



>FitnessBrowser__Cup4G11:RR42_RS18500
          Length = 492

 Score =  436 bits (1120), Expect = e-126
 Identities = 226/472 (47%), Positives = 303/472 (64%), Gaps = 4/472 (0%)

Query: 40  SPSNNQEIAKVTEVSMEEYEEGLRSCNDAAKTWKSLPAPKRGEIVRQIGDALREKLQHLG 99
           SP + +    +   S+ E +  +        +W  +PAP RGE+VR+ G+ LRE  +HLG
Sbjct: 19  SPIDGEAFGHLPACSLAEADARIERARVMQASWALVPAPVRGEVVRRFGEVLREHKKHLG 78

Query: 100 KLVSLEMGKILAEGIGEVQEVIYMCDFAVGLSRQLNGSIIPSERPDHMMFEVWNPLGIVG 159
           +LVSLE GKIL EG+GEVQE+I +CDFAVGLSRQL+G  I SERP H M E W+P G+ G
Sbjct: 79  ELVSLEAGKILQEGLGEVQEMIDICDFAVGLSRQLHGLTIASERPQHAMRETWHPYGLCG 138

Query: 160 VITAFNFPCAVLGWNACIALVCGNCVVWKGAPTTPLVTIAVTKLIAEVLE-KNNLPAAIF 218
           VI+AFNFP AV  WNA +ALVCGN V+WK +  TPL  +A+  L+  VLE        I 
Sbjct: 139 VISAFNFPVAVWAWNAALALVCGNGVIWKPSEKTPLTALAMQSLLDGVLEIAAPQHVGIA 198

Query: 219 TAFCGGAEIGEAIAKDTRIPLVSFTGSSKVGAKVQQIVTERFGKCLLELSGNNALIVMDD 278
           T   GG  +G+ + +   + LVS TGS+++G  V     ERF + +LEL GNNA I+   
Sbjct: 199 TVLSGGPALGQHLVEHAAVRLVSATGSTRMGRAVGIACAERFKRAILELGGNNAAIIAPS 258

Query: 279 ADVGLAVRSIFFAAVGTAGQRCTTCRRLYLHESIYQNVLDKLVGLYNQVKIGDPLEEGTL 338
           AD+ LAVR++ F+A GTAGQRCT+ RR ++H  + + V  +L+ ++ ++ +GDPL E TL
Sbjct: 259 ADLELAVRAMTFSAAGTAGQRCTSLRRAFVHVDVLEAVTTRLIQVFGRLPVGDPLAETTL 318

Query: 339 VGPVHTKASRENFEKGISTIKSQGGKILTGGSVIES---DGNFVQPTIVEIASNASVVKE 395
           VGP+   A+       +   +  G  +  G  V+     +  +V+P +V        +  
Sbjct: 319 VGPLIDGAAGAAMAAALLRCREHGNTVHGGERVLAEKYPNAEYVRPALVLTDRQHETMLS 378

Query: 396 ELFGPVLYVMKFKTLEEAIALNNSVPQGLSSSIFTSKPNTIFKWIGPHGSDCGIVNVNIP 455
           E F P+LYVM + TL+EAIALNN+   GLSS IFT       +++   GSDCGI NVNI 
Sbjct: 379 ETFAPILYVMPYTTLDEAIALNNASEHGLSSCIFTESLREAERFMSASGSDCGIANVNIG 438

Query: 456 TNGAEIGGAFGGEKATGGGREAGSDSWKQYMRRSTCTINYGTELPLAQGINF 507
           T+GAEIGGAFGGEKATGGGRE+GSD+WK YMRR+T T+NYG  LPLAQG+ F
Sbjct: 439 TSGAEIGGAFGGEKATGGGRESGSDAWKGYMRRATNTVNYGDALPLAQGVRF 490


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: 731
Number of extensions: 32
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: 492
Length adjustment: 34
Effective length of query: 474
Effective length of database: 458
Effective search space:   217092
Effective search space used:   217092
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 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