GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kce in Thioclava dalianensis DLFJ1-1

Align 3-keto-5-aminohexanoate cleavage enzyme (EC 2.3.1.247) (characterized)
to candidate WP_038069183.1 DL1_RS18540 3-keto-5-aminohexanoate cleavage protein

Query= BRENDA::Q8RHX2
         (272 letters)



>NCBI__GCF_000715505.1:WP_038069183.1
          Length = 310

 Score =  148 bits (374), Expect = 1e-40
 Identities = 100/300 (33%), Positives = 158/300 (52%), Gaps = 34/300 (11%)

Query: 4   KLIITAAICGAEVTKEHNPAVPYTVEEIAREAESAYKAGASIIHLHVRE-DDGTPTQDKE 62
           K II+ AI GA  T   + A+PYT ++IA ++ +A +AGASI+HLH R  +DG  + D +
Sbjct: 6   KTIISCAITGAIHTPTMSDALPYTADDIASQSIAAAEAGASILHLHARRPEDGGVSVDPD 65

Query: 63  RFRKCIEAIREKCPDVIIQPSTGGAVGMTDLERLQPT-ELHPEMATLDCGTCNFG----- 116
            F   +  I++   D ++  STGG++ +   ER++P     PEM +++ G+ NF      
Sbjct: 66  HFAAFLPRIKQ-ATDAVVNISTGGSLHLPISERIKPALTFSPEMCSMNMGSMNFSFHPLA 124

Query: 117 ------------------GDEIFVNTENTIKNFGKILIERGVKPEIEVFDKGMIDYAIRY 158
                                IF NT   I+     L    +K E E +D G + Y +++
Sbjct: 125 KRYDDWKFDWEKDYVESSEGNIFRNTFADIREAATSLAPHDIKFEHECYDVGHL-YNLKF 183

Query: 159 QKQ-GFIQKPMHFDFVLGVQ--MSASARDLVFMSESIP----EGSTWTVAGVGRHQFQMA 211
               G  + P+   F+ G+   +     +L+FM  +      +   W+V G G  Q  +A
Sbjct: 184 CMDIGLFKAPIFIQFIFGILGGIGPEVDNLIFMKRTADRLFGDDYRWSVLGAGGAQMGLA 243

Query: 212 ALAIVMGGHVRVGFEDNVYIDKGILAKSNGELVERVVRLAKELGREIATPDEARQILSLK 271
           + A  MGG++RVG ED++ I +G LA+SN + V ++ R+ ++LG EIATPDEAR IL LK
Sbjct: 244 STAAQMGGNLRVGLEDSLLIRRGQLAESNAQQVAKIRRIVEDLGSEIATPDEARDILGLK 303


Lambda     K      H
   0.319    0.137    0.394 

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: 205
Number of extensions: 9
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: 272
Length of database: 310
Length adjustment: 26
Effective length of query: 246
Effective length of database: 284
Effective search space:    69864
Effective search space used:    69864
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 (21.8 bits)
S2: 48 (23.1 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