GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Pseudomonas fluorescens FW300-N2E3

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate AO353_09195 AO353_09195 aldehyde dehydrogenase

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



>FitnessBrowser__pseudo3_N2E3:AO353_09195
          Length = 497

 Score =  947 bits (2449), Expect = 0.0
 Identities = 471/497 (94%), Positives = 487/497 (97%)

Query: 1   MTTLTRADWEQRARDLKIEGRAFINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQ 60
           MTTLTRADWEQRARDLKIEGRA+INGEYT AVSGETFDC+SPVDGRLLGKIASCD ADAQ
Sbjct: 1   MTTLTRADWEQRARDLKIEGRAYINGEYTAAVSGETFDCISPVDGRLLGKIASCDAADAQ 60

Query: 61  RAVENARATFSSGVWSRLAPSKRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNID 120
           RAVENAR+TF+SGVWSRLAP+KRKATMIRFAGLLKQHAEELALLETLDMGKPISDSL ID
Sbjct: 61  RAVENARSTFNSGVWSRLAPAKRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLYID 120

Query: 121 VPGAAQALSWSGEAIDKLYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP 180
           VPGAAQALSWSGEAIDK+YDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP
Sbjct: 121 VPGAAQALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGP 180

Query: 181 ALSTGNSVVLKPSEKSPLTALRIAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTL 240
           ALSTGNSV+LKPSEKSPLTA+R+AALA+EAGIPKGVLNVLPGYGHTVGKALALHMDVDTL
Sbjct: 181 ALSTGNSVILKPSEKSPLTAIRLAALAVEAGIPKGVLNVLPGYGHTVGKALALHMDVDTL 240

Query: 241 VFTGSTKIAKQLMIYSGESNMKRIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGE 300
           VFTGSTKIAKQLMIYSGESNMKR+WLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGE
Sbjct: 241 VFTGSTKIAKQLMIYSGESNMKRVWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGE 300

Query: 301 VCTAGSRLLVERSIKDTFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAG 360
           VCTAGSRLLVERSIKD FLPLVIEALK WKPGNPLDPATNVGALVDTQQMNTVLSYIE+G
Sbjct: 301 VCTAGSRLLVERSIKDKFLPLVIEALKTWKPGNPLDPATNVGALVDTQQMNTVLSYIESG 360

Query: 361 HSDGAKLVAGGKRILEETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIE 420
           HSDGAKLVAGGKRIL+ETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVI FD+ E+AI 
Sbjct: 361 HSDGAKLVAGGKRILQETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVITFDSVEEAIR 420

Query: 421 IANDTPYGLAAAVWTKDISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS 480
           IANDTPYGLAAAVWT DISK HLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS
Sbjct: 421 IANDTPYGLAAAVWTSDISKGHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS 480

Query: 481 LHAFDKYTELKSTWIKL 497
           LHAFDKYTELK+TWIKL
Sbjct: 481 LHAFDKYTELKATWIKL 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: 993
Number of extensions: 33
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