GapMind for catabolism of small carbon sources

 

Alignments for a candidate for andAa in Pseudomonas simiae WCS417

Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate GFF2881 PS417_14730 nitrite reductase

Query= SwissProt::Q84BZ0
         (406 letters)



>FitnessBrowser__WCS417:GFF2881
          Length = 846

 Score = 91.3 bits (225), Expect = 1e-22
 Identities = 103/348 (29%), Positives = 146/348 (41%), Gaps = 34/348 (9%)

Query: 7   VIVGAGHAARRTAEALRARDA--DAPIVMIGAERELPYDRPALSKDALLNDDGEQRAFVR 64
           ++VG G         L  R A     + +   E    YDR  LS +     D E  A + 
Sbjct: 8   IVVGNGMVGHHCVAQLIERGALDHYRLHVFSEEPMRAYDRVHLS-EYFSGRDAESLA-LS 65

Query: 65  DAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPIDA-- 122
           DA+ Y    + L LG  V  I+R    V   DG  + Y KLVLATGS    F  PID   
Sbjct: 66  DASLYQTPGVTLHLGVPVLEIDRARCEVITADGC-VAYDKLVLATGSY--PFVPPIDGAE 122

Query: 123 GVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARLLQ 182
           G      RT+ D  A+R      RR  V+GGG +GLE A A + LG    V++ A RL+ 
Sbjct: 123 GDSRLVYRTLEDLDAIRKAAANARRGVVVGGGLLGLEAANALKSLGLEAHVVEFAPRLMP 182

Query: 183 RALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGD-VHADVVVVGIGV 241
             L +  G       +  GVG  ++   ++I A       +     + +  D++V   G+
Sbjct: 183 VQLDDFGGLALKAQIERLGVGVHLSRATQSISAGEHYRYRMNFANDEFLETDLIVFSAGI 242

Query: 242 LPNVELAQAAGLDVD--NGIRVDAGCRTADRAIFAAGEVTMHFNPLLGRHVRIESWQVAE 299
                LA+ AGLD+    G+ ++  C + D  I+A GE       L G  +    +Q+A 
Sbjct: 243 RAQDALARQAGLDIGPRGGVVINDECLSCDPNIYAIGECASWNGSLFG--LVAPGYQMAR 300

Query: 300 N----------QPAVAA-----ANLLGAD-----DAYAELPWLWSDQY 327
                      +P V A       LLG D     DA+A  P   S Q+
Sbjct: 301 GVAALLCKQTAEPFVGADMSTKLKLLGVDVGSIGDAHAHTPGARSYQF 348


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: 650
Number of extensions: 27
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: 406
Length of database: 846
Length adjustment: 36
Effective length of query: 370
Effective length of database: 810
Effective search space:   299700
Effective search space used:   299700
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 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