GapMind for catabolism of small carbon sources

 

Aligments for a candidate for antC in Pseudomonas fluorescens FW300-N2E3

Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate AO353_23545 AO353_23545 NADH oxidase

Query= reanno::WCS417:GFF4631
         (335 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_23545 AO353_23545 NADH
           oxidase
          Length = 337

 Score =  266 bits (681), Expect = 4e-76
 Identities = 140/338 (41%), Positives = 204/338 (60%), Gaps = 8/338 (2%)

Query: 1   MNHKVAFSFADGKTLFFPVGANEILLDAALRNGIKIPLDCREGVCGTCQGRCESGDYS-- 58
           M H +A +F DG T F      E + DAA R GI IPLDCR+G CGTC+   E+G Y   
Sbjct: 1   MTHSIALNFEDGVTRFVDANPGETVADAAYRQGINIPLDCRDGACGTCKCFAEAGRYDLG 60

Query: 59  QDYVDEEALSSLDLQQRKMLSCQTRVKSDATFYFDFDSSLCNAPGPVQVKGTVSAVEQVS 118
           ++Y+ E+ALSS + ++  +L+CQ R  SD        S +C           +S V Q+S
Sbjct: 61  EEYI-EDALSSDEAEKGFVLTCQMRALSDCVVRVPVSSDVCRTQ-KAHYSAAISQVRQLS 118

Query: 119 ASTAILQVQLD--QALDFLPGQYARLSVPGTDSWRSYSFANLPGN-HLQFLVRLLPDGVM 175
            ST  L ++ +    L FLPGQY  L +PG++  R+YSF++L  +  + FL+R +P G+M
Sbjct: 119 DSTIALSIKGEALSKLAFLPGQYVNLGIPGSEQTRAYSFSSLQRDGEVSFLIRNVPGGLM 178

Query: 176 SNYLRERCQVGDELLMEAPLGAFYLRHVTQPLVLVAGGTGLSALLGMLDQLAANGCEQPV 235
           S++L    + GD + +  PLG+FYLR + +PL+L+AGGTGL+    ML+++A  G E P+
Sbjct: 179 SSFLTGIAKAGDSMSLAGPLGSFYLRDIQRPLLLLAGGTGLAPFTAMLEKIAEQGSEYPL 238

Query: 236 HLYYGVRGAEDLCEAARIRAYAAKIPNLRYTEVLSAPSEEWSGKRGYLTEHFDLAELRDG 295
           HL YGV    DL E  R++A AA+IPN  ++  ++ P      K GY+T+H +   L DG
Sbjct: 239 HLIYGVTNDFDLVELDRLQALAARIPNFSFSACVANPQSAHPLK-GYVTQHIEPKHLNDG 297

Query: 296 SADMYLCGPPPMVESIQQWLADQALDGVQLYYEKFTQS 333
             D+YLCGPPPMVE++ Q++ +Q +     YYEKF  S
Sbjct: 298 DVDVYLCGPPPMVEAVSQFIREQGVSPKNFYYEKFAAS 335


Lambda     K      H
   0.320    0.136    0.412 

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: 338
Number of extensions: 12
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: 335
Length of database: 337
Length adjustment: 28
Effective length of query: 307
Effective length of database: 309
Effective search space:    94863
Effective search space used:    94863
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: 49 (23.5 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 paper from 2022 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