GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Maridesulfovibrio zosterae DSM 11974

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized)
to candidate WP_027723082.1 H589_RS0116710 3-oxoacyl-ACP reductase FabG

Query= SwissProt::Q1NEI6
         (249 letters)



>NCBI__GCF_000425265.1:WP_027723082.1
          Length = 240

 Score =  121 bits (304), Expect = 1e-32
 Identities = 80/241 (33%), Positives = 134/241 (55%), Gaps = 12/241 (4%)

Query: 11  RCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATH-----VVALDVS 65
           + A++TG + G+G  +A ++  +G  + L   + DA A   AE    H     ++  DV+
Sbjct: 3   KIALITGASKGIGAAIAVQLAEDGYDIWLNYRSDDAGAHKTAEQIKQHGQQCTLLKFDVT 62

Query: 66  DHAAVAAAAKDSAAALGKVD-ILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNR 124
           D  AV      S+    KV  I++ +AG T  ++ +     D + +V+ ++L G F   +
Sbjct: 63  DEKAVEENL--SSLLEKKVPYIVVNNAGFTRDSIMMMMDSSD-WNKVLQVHLTGFFNVTK 119

Query: 125 EVVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANAL 184
            VV  ML    GRI+N+AS +G+ G    + Y A+KAG+IG TKSL  E+A + ++ NA+
Sbjct: 120 PVVSRMLRKRTGRIINIASTSGETGVAGQTNYCAAKAGLIGATKSLAMEVAKRNILVNAV 179

Query: 185 TPATFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSG 244
           TP   ++ +L +LP   VD +++ IP+ RLG  +E A +V F+ S++ S+ T  T   +G
Sbjct: 180 TPGFIDTDMLSELP---VDEIKNTIPLKRLGTPKEVAGVVSFLCSDKASYITGQTIAVNG 236

Query: 245 G 245
           G
Sbjct: 237 G 237


Lambda     K      H
   0.318    0.132    0.381 

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: 140
Number of extensions: 5
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: 249
Length of database: 240
Length adjustment: 24
Effective length of query: 225
Effective length of database: 216
Effective search space:    48600
Effective search space used:    48600
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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