GapMind for catabolism of small carbon sources

 

Alignments for a candidate for andAa in Kocuria flava HO-9041

Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate WP_058857692.1 AS188_RS03580 pyridine nucleotide-disulfide oxidoreductase

Query= SwissProt::Q84BZ0
         (406 letters)



>NCBI__GCF_001482365.1:WP_058857692.1
          Length = 399

 Score =  190 bits (483), Expect = 6e-53
 Identities = 136/365 (37%), Positives = 178/365 (48%), Gaps = 21/365 (5%)

Query: 4   DPFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDG-EQRAF 62
           +  VIVGA  A    A A R       + ++G + + PYDRP LSKD L    G E  A 
Sbjct: 2   ESLVIVGASLAGLAAARAARNHGYTGRLTVVGEDPQRPYDRPPLSKDFLAGRIGAEDLAL 61

Query: 63  VRDAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDA 122
             +A   DA+ +   LG R  + +   + V LDDG  L    LV+ATG+  R+   PI  
Sbjct: 62  ETEADDLDAEWV---LGVRAVSFDAVTRTVVLDDGRLLHAEGLVVATGASPRSLP-PIAG 117

Query: 123 GVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQ 182
                 +RTVADA  LR  L  GRR+ V+G GFIG EVA+ A +LG  VTV++ +   L 
Sbjct: 118 LDNVVTLRTVADAHRLRELLAPGRRLVVVGAGFIGAEVASTAHELGLEVTVVEKSPTPLC 177

Query: 183 RALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRG-DVHADVVVVGIGV 241
             L   +GA    LH+  GV     T       A G    V    G  + ADVVVVGIG 
Sbjct: 178 GPLGAELGAVVAGLHERAGVELLCGTDIERFEVAGGAVRAVHLAGGRQLPADVVVVGIGA 237

Query: 242 LPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAENQ 301
            PN    + +G+++ NG+  DA  RT    + A G+    ++P  G H R+E W  A  +
Sbjct: 238 APNTAWLEGSGVELGNGVLCDAVGRTGVPGVVAVGDCAAWYDPATGTHRRVEHWTGAAER 297

Query: 302 PAVAAANLLGADDA---YAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFG 358
           PA+A   LLGAD A     + P+ WSDQY   LQ              GD ARG   V+ 
Sbjct: 298 PAIAVGALLGADPAELPAVKPPYFWSDQYGTRLQF------------AGDAARGDRIVYE 345

Query: 359 LGGDG 363
            GG G
Sbjct: 346 QGGPG 350


Lambda     K      H
   0.322    0.138    0.410 

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: 433
Number of extensions: 32
Number of successful extensions: 6
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: 406
Length of database: 399
Length adjustment: 31
Effective length of query: 375
Effective length of database: 368
Effective search space:   138000
Effective search space used:   138000
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: 50 (23.9 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