GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Williamsia sterculiae CPCC 203464

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_076476004.1 BW971_RS02050 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>NCBI__GCF_900156495.1:WP_076476004.1
          Length = 500

 Score =  392 bits (1008), Expect = e-113
 Identities = 225/471 (47%), Positives = 291/471 (61%), Gaps = 14/471 (2%)

Query: 56  RWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISVKERSSLLRKW 115
           R   T  TF V DPA+G +L  VAD G  +A  A++ +  A   W   S +ERS +LR  
Sbjct: 32  RTAATARTFVVDDPATGRELTQVADAGPDDAMLALKQSVAAADDWAATSPRERSVILRAA 91

Query: 116 YDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGDIIYTSAKDKR 175
           +DL+ +   +LA ++T E GK L +++ EI Y A FL WFSEEA R+ G    +     R
Sbjct: 92  FDLITERAADLALLMTLEMGKALPDSKSEIAYGAEFLRWFSEEAVRINGRYTQSPGGTGR 151

Query: 176 GLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSALALAQLANQA 235
            LV  QPVG    ITPWNFP AM TRK+G ALAAG T++VKPA +TP + LALA++  +A
Sbjct: 152 ILVTHQPVGPCLAITPWNFPLAMGTRKIGPALAAGNTIIVKPAAETPLTMLALAKIFAEA 211

Query: 236 GIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAANSVKRVSMEL 295
           G+PPGV  V+P S   A  V   L  D  + KI+FTGST  G+ILL  AA +V+R SMEL
Sbjct: 212 GLPPGVLAVLPTS--DASAVCTPLIEDTRIRKITFTGSTGVGRILLGQAAANVQRTSMEL 269

Query: 296 GGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFVTKFAE---AM 352
           GG APFIVFD A++D A+ GA A+K RN G+ C  +NRFLV    HDS   +F +   A 
Sbjct: 270 GGNAPFIVFDDADLDAALDGAFAAKMRNGGEACTAANRFLV----HDSVAEEFTDGLIAR 325

Query: 353 KKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGG-----KRHQSGGNF 407
            ++L VG G+ +GTT GPLI+EK    V + V DAVA GA V  GG     ++H   G F
Sbjct: 326 MQALTVGPGYADGTTLGPLISEKQRNSVAQKVTDAVADGARVRLGGEQARAEQHGGDGWF 385

Query: 408 FEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQIW 467
           + PT+L  V         E FGPVA +  F   +EA+A AN  + GLA Y Y++D  +  
Sbjct: 386 YPPTVLDEVPVGAEITRGEIFGPVAVISTFGTVDEAIAAANDTEYGLAAYIYTRDLDRAL 445

Query: 468 RVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYV 518
            V+++L+ G+VGVN G+IS V  PFGG KQSGLGREG   GI E+L  KYV
Sbjct: 446 SVSDRLQTGLVGVNRGVISDVAAPFGGEKQSGLGREGGLEGIGEFLTTKYV 496


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: 599
Number of extensions: 23
Number of successful extensions: 4
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: 500
Length adjustment: 35
Effective length of query: 488
Effective length of database: 465
Effective search space:   226920
Effective search space used:   226920
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 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