GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Lentibacillus jeotgali Grbi

Align long-chain-aldehyde dehydrogenase (EC 1.2.1.48) (characterized)
to candidate WP_010530889.1 ON01_RS09935 aldehyde dehydrogenase

Query= BRENDA::P51648
         (485 letters)



>NCBI__GCF_000224785.1:WP_010530889.1
          Length = 458

 Score =  381 bits (979), Expect = e-110
 Identities = 188/433 (43%), Positives = 286/433 (66%), Gaps = 2/433 (0%)

Query: 9   RQAFLSGRSRPLRFRLQQLEALRRMVQEREKDILTAIAADLCKSEFNVYSQEVITVLGEI 68
           R  FL+G++    FR +QL +L+ M++  +++I  A+  DL KSE+  ++ E+  +  +I
Sbjct: 14  RTFFLTGKTLDPAFRKEQLTSLKGMLKSYQQEIYHALKNDLNKSEYEAFTTELGYLYTDI 73

Query: 69  DFMLENLPEWVTAKPVKKNVLTMLDEAYIQPQPLGVVLIIGAWNYPFVLTIQPLIGAIAA 128
           DF L++L +WV+ + V+  +     ++YIQ +P GV LI+  WNYP  L I P IGAIAA
Sbjct: 74  DFALKHLKDWVSLEKVETPLTHKGSKSYIQKEPYGVTLIMAPWNYPLHLAIAPAIGAIAA 133

Query: 129 GNAVIIKPSELSENTAKILAKLLPQYLDQDLYIVINGGVEETTELLKQRFDHIFYTGNTA 188
           GN V++KPSEL+++T+ ILA ++    D   + V+ G  + + +LL+QR+D+IF+TG+T 
Sbjct: 134 GNTVVLKPSELTQSTSTILADMIRSTFDASYFTVVEGAKDVSQQLLEQRWDYIFFTGSTN 193

Query: 189 VGKIVMEAAAKHLTPVTLELGGKSPCYIDKDCDLDIVCRRITWGKYMNCGQTCIAPDYIL 248
           VGKIVME A+KHLTPVTLELGGKSP  +D+D  +D+  +RI WGK+ N GQTC+APDY+ 
Sbjct: 194 VGKIVMEQASKHLTPVTLELGGKSPAIVDQDAKIDLAAKRIVWGKFTNAGQTCVAPDYVY 253

Query: 249 CEASLQNQIVWKIKETVKEFYGENIKESPDYERIINLRHFKRILSLLEGQKIAFGGETDE 308
               ++ +++  +K+ +K  YG+   ++ DY RI+N +HF R+ + +   +I  GGE +E
Sbjct: 254 VHEKVKLKLLRAMKKHIKSLYGKKPVQNYDYVRIVNKQHFDRLNAFMTDGEIIHGGEINE 313

Query: 309 ATRYIAPTVLTDVDPKTKVMQEEIFGPILPIVPVKNVDEAINFINEREKPLALYVFSHNH 368
               I PT+L  ++    +MQEEIFGP+LP++   ++D+ I+ + E EKPLALY F  N 
Sbjct: 314 EKLTIEPTILDKINWDDAIMQEEIFGPLLPVMTFSSLDDLISEMKEMEKPLALYYFGENE 373

Query: 369 KLIKRMIDETSSGGVTGNDVIMHFTLNSFPFGGVGSSGMGAYHGKHSFDTFSHQRPCLLK 428
              ++++   S GG   ND + H      PFGGVG+SGMGAYHGK+SFDTFSH++  L +
Sbjct: 374 LKQQKLMLNVSFGGGCINDTLYHLANPHLPFGGVGNSGMGAYHGKYSFDTFSHRKSILKQ 433

Query: 429 SLKREGANKLRYP 441
           + K +     RYP
Sbjct: 434 TTKFD--IPFRYP 444


Lambda     K      H
   0.321    0.139    0.411 

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: 569
Number of extensions: 22
Number of successful extensions: 1
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: 485
Length of database: 458
Length adjustment: 33
Effective length of query: 452
Effective length of database: 425
Effective search space:   192100
Effective search space used:   192100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 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