GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glaH in Escherichia coli BW25113

Align Glutarate 2-hydroxylase; G-2-H; Carbon starvation induced protein D; EC 1.14.11.- (characterized)
to candidate 16749 b2659 orf, hypothetical protein (VIMSS)

Query= SwissProt::P76621
         (325 letters)



>FitnessBrowser__Keio:16749
          Length = 325

 Score =  660 bits (1702), Expect = 0.0
 Identities = 325/325 (100%), Positives = 325/325 (100%)

Query: 1   MNALTAVQNNAVDSGQDYSGFTLTPSAQSPRLLELTFTEQTTKQFLEQVAEWPVQALEYK 60
           MNALTAVQNNAVDSGQDYSGFTLTPSAQSPRLLELTFTEQTTKQFLEQVAEWPVQALEYK
Sbjct: 1   MNALTAVQNNAVDSGQDYSGFTLTPSAQSPRLLELTFTEQTTKQFLEQVAEWPVQALEYK 60

Query: 61  SFLRFRVAKILDDLCANQLQPLLLKTLLNRAEGALLINAVGVDDVKQADEMVKLATAVAH 120
           SFLRFRVAKILDDLCANQLQPLLLKTLLNRAEGALLINAVGVDDVKQADEMVKLATAVAH
Sbjct: 61  SFLRFRVAKILDDLCANQLQPLLLKTLLNRAEGALLINAVGVDDVKQADEMVKLATAVAH 120

Query: 121 LIGRSNFDAMSGQYYARFVVKNVDNSDSYLRQPHRVMELHNDGTYVEEITDYVLMMKIDE 180
           LIGRSNFDAMSGQYYARFVVKNVDNSDSYLRQPHRVMELHNDGTYVEEITDYVLMMKIDE
Sbjct: 121 LIGRSNFDAMSGQYYARFVVKNVDNSDSYLRQPHRVMELHNDGTYVEEITDYVLMMKIDE 180

Query: 181 QNMQGGNSLLLHLDDWEHLDNYFRHPLARRPMRFAAPPSKNVSKDVFHPVFDVDQQGRPV 240
           QNMQGGNSLLLHLDDWEHLDNYFRHPLARRPMRFAAPPSKNVSKDVFHPVFDVDQQGRPV
Sbjct: 181 QNMQGGNSLLLHLDDWEHLDNYFRHPLARRPMRFAAPPSKNVSKDVFHPVFDVDQQGRPV 240

Query: 241 MRYIDQFVQPKDFEEGVWLSELSDAIETSKGILSVPVPVGKFLLINNLFWLHGRDRFTPH 300
           MRYIDQFVQPKDFEEGVWLSELSDAIETSKGILSVPVPVGKFLLINNLFWLHGRDRFTPH
Sbjct: 241 MRYIDQFVQPKDFEEGVWLSELSDAIETSKGILSVPVPVGKFLLINNLFWLHGRDRFTPH 300

Query: 301 PDLRRELMRQRGYFAYASNHYQTHQ 325
           PDLRRELMRQRGYFAYASNHYQTHQ
Sbjct: 301 PDLRRELMRQRGYFAYASNHYQTHQ 325


Lambda     K      H
   0.321    0.136    0.405 

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: 506
Number of extensions: 8
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: 325
Length of database: 325
Length adjustment: 28
Effective length of query: 297
Effective length of database: 297
Effective search space:    88209
Effective search space used:    88209
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: 48 (23.1 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