GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Pseudomonas fluorescens FW300-N2C3

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate AO356_24600 AO356_24600 ketoglutarate semialdehyde dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_612
         (526 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24600 AO356_24600
           ketoglutarate semialdehyde dehydrogenase
          Length = 526

 Score = 1031 bits (2666), Expect = 0.0
 Identities = 522/526 (99%), Positives = 523/526 (99%)

Query: 1   MNQILGHNYIGGARSAAGQTRLQSVDASTGEALPHDFIQATAEEVDAAAKAAAAAYPAYR 60
           MNQILGHNYIGGARSAAGQTRLQS DASTGEALPHDFIQATAEEVDAAAKAAAAAYPAYR
Sbjct: 1   MNQILGHNYIGGARSAAGQTRLQSADASTGEALPHDFIQATAEEVDAAAKAAAAAYPAYR 60

Query: 61  SLSAVRRAEFLEAIADELDALGDEFVAVVCRETALPAARIQGERGRTSGQMRLFAKVLRR 120
           SLSAVRRAEFLEAIADELDALGDEFVAVVCRETALPAARIQGERGRTSGQMRLFAKVLRR
Sbjct: 61  SLSAVRRAEFLEAIADELDALGDEFVAVVCRETALPAARIQGERGRTSGQMRLFAKVLRR 120

Query: 121 GDFYGARIDRALPERTPLPRPDLRQYRIGLGPVAVFGASNFPLAFSTAGGDTASALAAGC 180
           GDFYGARIDRALPERTPLPRPDLRQYRIGLGPVAVFGASNFPLAFSTAGGDTASALAAGC
Sbjct: 121 GDFYGARIDRALPERTPLPRPDLRQYRIGLGPVAVFGASNFPLAFSTAGGDTASALAAGC 180

Query: 181 PVVFKAHSGHMATAEHVADAIIRAAEKTLMPAGVFNMIYGGGVGEWLVKHPAIQAVGFTG 240
           PVVFKAHSGHMATAEHVADAIIRAAEKT MPAGVFNMIYGGGVGEWLVKHPAIQAVGFTG
Sbjct: 181 PVVFKAHSGHMATAEHVADAIIRAAEKTAMPAGVFNMIYGGGVGEWLVKHPAIQAVGFTG 240

Query: 241 SLKGGRALCDMAAARPQPIPVFAEMSSINPVIVLPQALETRAESVARDLTASVVQGCGQF 300
           SLKGGRALCDMAAARPQPIPVFAEMSSINPVIVLPQALETRAESVARDLTASVVQGCGQF
Sbjct: 241 SLKGGRALCDMAAARPQPIPVFAEMSSINPVIVLPQALETRAESVARDLTASVVQGCGQF 300

Query: 301 CTNPGLVIGIRSPQFTAFTQQVAALIGDQAPQTMLNAGTLQSYGKGLQKLLAHPGIEHLA 360
           CTNPGLVIGIRSPQFTAFTQQVAALIGDQAPQTMLNAGTLQSYGKGLQKLLAHPGIEHLA
Sbjct: 301 CTNPGLVIGIRSPQFTAFTQQVAALIGDQAPQTMLNAGTLQSYGKGLQKLLAHPGIEHLA 360

Query: 361 GRQQQGNQAQPQLFKADASLLINGDEALQEEVFGPTTVFVEVADQAQLTAALNGLHGQLT 420
           GR+QQGNQAQPQLFKADASLLINGDEALQEEVFGPTTVFVEVADQAQLTAALNGLHGQLT
Sbjct: 361 GREQQGNQAQPQLFKADASLLINGDEALQEEVFGPTTVFVEVADQAQLTAALNGLHGQLT 420

Query: 421 ATMIGEPADFERFSELTPLLEQKVGRILLNGYPTGVEVCDSMVHGGPYPATSDARGTSVG 480
           ATMIGEPADFERF ELTPLLEQKVGRILLNGYPTGVEVCDSMVHGGPYPATSDARGTSVG
Sbjct: 421 ATMIGEPADFERFGELTPLLEQKVGRILLNGYPTGVEVCDSMVHGGPYPATSDARGTSVG 480

Query: 481 TLAIDRFLRPVCFQNYPDSLLPEPLKNANPLGILRLVDGVPGREAL 526
           TLAIDRFLRPVCFQNYPDSLLPEPLKNANPLGILRLVDGVPGREAL
Sbjct: 481 TLAIDRFLRPVCFQNYPDSLLPEPLKNANPLGILRLVDGVPGREAL 526


Lambda     K      H
   0.319    0.135    0.395 

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: 1123
Number of extensions: 30
Number of successful extensions: 2
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: 526
Length of database: 526
Length adjustment: 35
Effective length of query: 491
Effective length of database: 491
Effective search space:   241081
Effective search space used:   241081
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: 52 (24.6 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