GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolJ in Pseudomonas fluorescens FW300-N2C3

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 AO356_23160 AO356_23160 5-dehydro-2-deoxygluconokinase

Query= reanno::pseudo5_N2C3_1:AO356_23160
         (645 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23160
          Length = 645

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

Query: 1   MGQTRFASGRQLDVICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLR 60
           MGQTRFASGRQLDVICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLR
Sbjct: 1   MGQTRFASGRQLDVICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLR 60

Query: 61  SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTAMVLLGIKDRETFPLVFYRENC 120
           SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTAMVLLGIKDRETFPLVFYRENC
Sbjct: 61  SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTAMVLLGIKDRETFPLVFYRENC 120

Query: 121 ADMALRAEDIDETFIASSKALLITGTHFSTDGVYKASIQALDYAQKHQVKRVLDIDYRPV 180
           ADMALRAEDIDETFIASSKALLITGTHFSTDGVYKASIQALDYAQKHQVKRVLDIDYRPV
Sbjct: 121 ADMALRAEDIDETFIASSKALLITGTHFSTDGVYKASIQALDYAQKHQVKRVLDIDYRPV 180

Query: 181 LWGLASKADGETRFVADQKVSQHVQSILPRFDLIVGTEEEFLIAGGSEDLLTALRTVRSL 240
           LWGLASKADGETRFVADQKVSQHVQSILPRFDLIVGTEEEFLIAGGSEDLLTALRTVRSL
Sbjct: 181 LWGLASKADGETRFVADQKVSQHVQSILPRFDLIVGTEEEFLIAGGSEDLLTALRTVRSL 240

Query: 241 TAATLVVKLGPQGCTVIHGAIPARLEDGAIYPGVRVEVLNVLGAGDAFMSGFLAGWLEDA 300
           TAATLVVKLGPQGCTVIHGAIPARLEDGAIYPGVRVEVLNVLGAGDAFMSGFLAGWLEDA
Sbjct: 241 TAATLVVKLGPQGCTVIHGAIPARLEDGAIYPGVRVEVLNVLGAGDAFMSGFLAGWLEDA 300

Query: 301 SDERCCQLANACGGLVVSRHACAPAMPTRAELDYLFDSPVPITRPDQDVVLQRLHQVSVP 360
           SDERCCQLANACGGLVVSRHACAPAMPTRAELDYLFDSPVPITRPDQDVVLQRLHQVSVP
Sbjct: 301 SDERCCQLANACGGLVVSRHACAPAMPTRAELDYLFDSPVPITRPDQDVVLQRLHQVSVP 360

Query: 361 RKTWKQLFIFAFDHRGQLVELAQKGGRELSSIGELKQLFIQAVARVEADLRHQGIEADVG 420
           RKTWKQLFIFAFDHRGQLVELAQKGGRELSSIGELKQLFIQAVARVEADLRHQGIEADVG
Sbjct: 361 RKTWKQLFIFAFDHRGQLVELAQKGGRELSSIGELKQLFIQAVARVEADLRHQGIEADVG 420

Query: 421 LLADQRFGQDSLNAATGRGWWVARPVEVQGSRPLAFEHGRSIGSNLIAWPQEQIIKCLVQ 480
           LLADQRFGQDSLNAATGRGWWVARPVEVQGSRPLAFEHGRSIGSNLIAWPQEQIIKCLVQ
Sbjct: 421 LLADQRFGQDSLNAATGRGWWVARPVEVQGSRPLAFEHGRSIGSNLIAWPQEQIIKCLVQ 480

Query: 481 FHPDDEPLLRLEQEAQLMGLYKASEASGHELLLEVIPPKDHPSPHPDVLYRALKRLYNLG 540
           FHPDDEPLLRLEQEAQLMGLYKASEASGHELLLEVIPPKDHPSPHPDVLYRALKRLYNLG
Sbjct: 481 FHPDDEPLLRLEQEAQLMGLYKASEASGHELLLEVIPPKDHPSPHPDVLYRALKRLYNLG 540

Query: 541 IFPAWWKIEAQGADEWQQLDELIQQRDPYCRGVVLLGLNAPAAALAEGFRQASQSSTCRG 600
           IFPAWWKIEAQGADEWQQLDELIQQRDPYCRGVVLLGLNAPAAALAEGFRQASQSSTCRG
Sbjct: 541 IFPAWWKIEAQGADEWQQLDELIQQRDPYCRGVVLLGLNAPAAALAEGFRQASQSSTCRG 600

Query: 601 FAVGRTIFQEPSRAWLAGEIDDETLIQQVQGRFVELIEAWRAARS 645
           FAVGRTIFQEPSRAWLAGEIDDETLIQQVQGRFVELIEAWRAARS
Sbjct: 601 FAVGRTIFQEPSRAWLAGEIDDETLIQQVQGRFVELIEAWRAARS 645


Lambda     K      H
   0.322    0.137    0.413 

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: 1464
Number of extensions: 41
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 (21.9 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:

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