GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB in Pseudomonas fluorescens FW300-N2E2

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Pf6N2E2_4383 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= reanno::pseudo6_N2E2:Pf6N2E2_4383
         (497 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4383
          Length = 497

 Score =  984 bits (2544), Expect = 0.0
 Identities = 497/497 (100%), Positives = 497/497 (100%)

Query: 1   MTTLTRADWEQRARDLKIEGRAFINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQ 60
           MTTLTRADWEQRARDLKIEGRAFINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQ
Sbjct: 1   MTTLTRADWEQRARDLKIEGRAFINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQ 60

Query: 61  RAVENARATFSSGVWSRLAPSKRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNID 120
           RAVENARATFSSGVWSRLAPSKRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNID
Sbjct: 61  RAVENARATFSSGVWSRLAPSKRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNID 120

Query: 121 VPGAAQALSWSGEAIDKLYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP 180
           VPGAAQALSWSGEAIDKLYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP
Sbjct: 121 VPGAAQALSWSGEAIDKLYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP 180

Query: 181 ALSTGNSVVLKPSEKSPLTALRIAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTL 240
           ALSTGNSVVLKPSEKSPLTALRIAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTL
Sbjct: 181 ALSTGNSVVLKPSEKSPLTALRIAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTL 240

Query: 241 VFTGSTKIAKQLMIYSGESNMKRIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGE 300
           VFTGSTKIAKQLMIYSGESNMKRIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGE
Sbjct: 241 VFTGSTKIAKQLMIYSGESNMKRIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGE 300

Query: 301 VCTAGSRLLVERSIKDTFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAG 360
           VCTAGSRLLVERSIKDTFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAG
Sbjct: 301 VCTAGSRLLVERSIKDTFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAG 360

Query: 361 HSDGAKLVAGGKRILEETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIE 420
           HSDGAKLVAGGKRILEETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIE
Sbjct: 361 HSDGAKLVAGGKRILEETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIE 420

Query: 421 IANDTPYGLAAAVWTKDISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS 480
           IANDTPYGLAAAVWTKDISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS
Sbjct: 421 IANDTPYGLAAAVWTKDISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS 480

Query: 481 LHAFDKYTELKSTWIKL 497
           LHAFDKYTELKSTWIKL
Sbjct: 481 LHAFDKYTELKSTWIKL 497


Lambda     K      H
   0.316    0.132    0.389 

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: 1002
Number of extensions: 26
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: 497
Length of database: 497
Length adjustment: 34
Effective length of query: 463
Effective length of database: 463
Effective search space:   214369
Effective search space used:   214369
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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:

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