GapMind for catabolism of small carbon sources

 

Aligments for a candidate for andAa in Marinobacter adhaerens HP15

Align Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component; EC 1.18.1.3 (characterized)
to candidate GFF27 HP15_27 FAD-dependent pyridine nucleotide-disulfide oxidoreductase

Query= SwissProt::Q84BZ0
         (406 letters)



>lcl|FitnessBrowser__Marino:GFF27 HP15_27 FAD-dependent pyridine
           nucleotide-disulfide oxidoreductase
          Length = 432

 Score =  196 bits (497), Expect = 1e-54
 Identities = 140/387 (36%), Positives = 195/387 (50%), Gaps = 5/387 (1%)

Query: 1   MSADPFVIVGAGHAARRTAEALRARDADAPIVMIGAERELPYDRPALSKDALLNDDGEQR 60
           MS     IVGAG A  + A +LR       I +IG E +LPY RP LSK  +L     + 
Sbjct: 23  MSLSSVAIVGAGQAGFQVAASLRQGGFKGKISLIGDEPDLPYQRPPLSKAYMLGKIKRES 82

Query: 61  AFVRDAAWYDAQRIALRLGTRVDAIEREAQRVRLDDGTTLPYAKLVLATGSRVRTFGGPI 120
              R   ++  Q I L   T ++ I+R+ +RV L  GT   Y  LVLATG+  R    P 
Sbjct: 83  LAFRPETFFQEQDIDLIHDTAIE-IDRQNRRVVLQSGTVCHYDHLVLATGAHNRPLALPG 141

Query: 121 DAGVVAHYVRTVADARALRAQLVRGRRVAVLGGGFIGLEVAAAARQLGCNVTVIDPAARL 180
           +       ++T+ DA AL  ++   R V V+G GFIGLE AA A Q   NV VID   R 
Sbjct: 142 EDLQGVFGIKTLKDADALSPEVKSARDVVVIGAGFIGLEFAAIAVQ-NANVQVIDMGQRA 200

Query: 181 LQRALPEVVGAYAHRLHDERGVGFQMATLPRAIRAAAGGGAIVETDRGDV-HADVVVVGI 239
           + RA+ + +       H E GV F      + +  + G    VE + G++  AD+VV GI
Sbjct: 201 MARAISQEMSEVFEETHQEWGVTFHFNQGVKRLIGSNGKVTGVEKEDGEILKADLVVYGI 260

Query: 240 GVLPNVELAQAAGLDVDNGIRVDAGCRTADRAIFAAGEVT-MHFNPLLGRHVRIESWQVA 298
           GV+PN+ +A  AGL ++NGI+VD+   T D  I A G+V         G+  RIES   A
Sbjct: 261 GVVPNIAIASEAGLTIENGIKVDSNLLTNDPHISAIGDVACFPCTHNEGQFTRIESVPNA 320

Query: 299 ENQPAVAAANLLGADDAYAELPWLWSDQYDCNLQMLGLFGAGQTTVVRGDPARGPFTVFG 358
            +Q    AA LLG+   ++ +PW W+DQ +  LQ+ GL     TTV  G      F+V  
Sbjct: 321 MDQARAVAARLLGSPSPFSSVPWFWTDQGNLKLQIAGLSTGFDTTVTLGSKDSRQFSVLC 380

Query: 359 LGGDGRIVAAAAVNLGRDIGAARRLIA 385
               G  VA  A N   D  A +++++
Sbjct: 381 F-RKGHFVAVEACNRPGDHLAGKKILS 406


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: 331
Number of extensions: 17
Number of successful extensions: 5
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: 432
Length adjustment: 32
Effective length of query: 374
Effective length of database: 400
Effective search space:   149600
Effective search space used:   149600
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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