GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iolJ in Pseudomonas simiae WCS417

Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29) (characterized)
to candidate GFF2324 PS417_11850 5-dehydro-2-deoxygluconokinase

Query= reanno::WCS417:GFF2324
         (645 letters)



>lcl|FitnessBrowser__WCS417:GFF2324 PS417_11850
           5-dehydro-2-deoxygluconokinase
          Length = 645

 Score = 1284 bits (3323), Expect = 0.0
 Identities = 645/645 (100%), Positives = 645/645 (100%)

Query: 1   MGQTRFASGRQLDLICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLR 60
           MGQTRFASGRQLDLICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLR
Sbjct: 1   MGQTRFASGRQLDLICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLR 60

Query: 61  SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTALVLLGLKDRETFPLVFYRENC 120
           SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTALVLLGLKDRETFPLVFYRENC
Sbjct: 61  SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTALVLLGLKDRETFPLVFYRENC 120

Query: 121 ADMALRAEDISEAFIASSKALLITGTHFSTDGVYKASIQALDYAAKHNVQRVLDIDYRPV 180
           ADMALRAEDISEAFIASSKALLITGTHFSTDGVYKASIQALDYAAKHNVQRVLDIDYRPV
Sbjct: 121 ADMALRAEDISEAFIASSKALLITGTHFSTDGVYKASIQALDYAAKHNVQRVLDIDYRPV 180

Query: 181 LWGLAGKADGETRFVADQNVSQHVQKILPRFDLIVGTEEEFLIAGGSEDLLTALRKVREL 240
           LWGLAGKADGETRFVADQNVSQHVQKILPRFDLIVGTEEEFLIAGGSEDLLTALRKVREL
Sbjct: 181 LWGLAGKADGETRFVADQNVSQHVQKILPRFDLIVGTEEEFLIAGGSEDLLTALRKVREL 240

Query: 241 TQATLVVKLGPQGCTVIHGAIPARLEDGAIYPGVRVEVLNVLGAGDAFMSGFLSGWINDA 300
           TQATLVVKLGPQGCTVIHGAIPARLEDGAIYPGVRVEVLNVLGAGDAFMSGFLSGWINDA
Sbjct: 241 TQATLVVKLGPQGCTVIHGAIPARLEDGAIYPGVRVEVLNVLGAGDAFMSGFLSGWINDA 300

Query: 301 SDERCSQLANACGGLVVSRHACAPAMPTPAELEYLFNSPVPITRPDQDLTLQRLHRVTVP 360
           SDERCSQLANACGGLVVSRHACAPAMPTPAELEYLFNSPVPITRPDQDLTLQRLHRVTVP
Sbjct: 301 SDERCSQLANACGGLVVSRHACAPAMPTPAELEYLFNSPVPITRPDQDLTLQRLHRVTVP 360

Query: 361 RKAWKQLFVFAFDHRWQLVDLAQKGGQDLARISDAKQLFIQAIERVEKKLAEQGVEADVG 420
           RKAWKQLFVFAFDHRWQLVDLAQKGGQDLARISDAKQLFIQAIERVEKKLAEQGVEADVG
Sbjct: 361 RKAWKQLFVFAFDHRWQLVDLAQKGGQDLARISDAKQLFIQAIERVEKKLAEQGVEADVG 420

Query: 421 LLADQRFGQDALNAASGRGWWIARPVEVQNSRPLAFEHGRSVGSNLIAWPQEQIIKCLVQ 480
           LLADQRFGQDALNAASGRGWWIARPVEVQNSRPLAFEHGRSVGSNLIAWPQEQIIKCLVQ
Sbjct: 421 LLADQRFGQDALNAASGRGWWIARPVEVQNSRPLAFEHGRSVGSNLIAWPQEQIIKCLVQ 480

Query: 481 FHPDDEPLLRLEQEAQLKAVYEASIVSGHELLLEVIPPKDHPSTYPDVLYRSLKRLYNLG 540
           FHPDDEPLLRLEQEAQLKAVYEASIVSGHELLLEVIPPKDHPSTYPDVLYRSLKRLYNLG
Sbjct: 481 FHPDDEPLLRLEQEAQLKAVYEASIVSGHELLLEVIPPKDHPSTYPDVLYRSLKRLYNLG 540

Query: 541 IYPAWWKIEAQSAEDWKKLDELIQERDPYCRGVVLLGLNASAEFLADGFQQASQSTTCRG 600
           IYPAWWKIEAQSAEDWKKLDELIQERDPYCRGVVLLGLNASAEFLADGFQQASQSTTCRG
Sbjct: 541 IYPAWWKIEAQSAEDWKKLDELIQERDPYCRGVVLLGLNASAEFLADGFQQASQSTTCRG 600

Query: 601 FAVGRTIFQEPSRAWMAGEIDDEVLIQQVQATFEQLINAWRSARN 645
           FAVGRTIFQEPSRAWMAGEIDDEVLIQQVQATFEQLINAWRSARN
Sbjct: 601 FAVGRTIFQEPSRAWMAGEIDDEVLIQQVQATFEQLINAWRSARN 645


Lambda     K      H
   0.321    0.137    0.409 

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: 1485
Number of extensions: 31
Number of successful extensions: 1
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: 645
Length of database: 645
Length adjustment: 38
Effective length of query: 607
Effective length of database: 607
Effective search space:   368449
Effective search space used:   368449
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: 54 (25.4 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