Alignments for a candidate for patA in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for patA in Pseudomonas fluorescens FW300-N1B4

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate Pf1N1B4_2257 Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)

Query= BRENDA::Q9I6J2
         (456 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2257
          Length = 400

 Score =  647 bits (1668), Expect = 0.0
 Identities = 297/371 (80%), Positives = 339/371 (91%)

Query: 7   NAKTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVN 66
           N +TREWQALS DHHL PF+D+KQL EKG RIIT A+GVY+WDSEGNKILD MAGLWCV 
Sbjct: 5   NPQTREWQALSSDHHLAPFSDFKQLKEKGPRIITSAKGVYLWDSEGNKILDGMAGLWCVA 64

Query: 67  VGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEA 126
           +GYGR+EL  AA++QMRELP+YNLFFQTAHPPV+ELAK I+DVAPEGMNHVFFTGSGSE 
Sbjct: 65  IGYGRDELADAASKQMRELPYYNLFFQTAHPPVLELAKVISDVAPEGMNHVFFTGSGSEG 124

Query: 127 NDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHI 186
           NDT+LRMVRHYWA KGQP+KKV+I R NGYHGSTVAG SLGGM  +HEQGD PIPGIVHI
Sbjct: 125 NDTMLRMVRHYWAIKGQPKKKVIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHI 184

Query: 187 AQPYWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWP 246
           AQPYW+GEGGDM+P+EFG+WAA QLE+KILEVG +NV AFIAEPIQGAGGVI+PPD+YWP
Sbjct: 185 AQPYWFGEGGDMTPNEFGIWAANQLEEKILEVGVDNVGAFIAEPIQGAGGVIIPPDSYWP 244

Query: 247 KIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVR 306
           +I+EILAKYDILF+ADEVICGFGRTGEWFG+ +Y   P +M IAKGLTSGYIPMGG++VR
Sbjct: 245 RIKEILAKYDILFVADEVICGFGRTGEWFGTDFYDLKPHMMTIAKGLTSGYIPMGGLIVR 304

Query: 307 DEIVEVLNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQEL 366
           D++VEVLN+GG+F HGFTYSGHPVAAAVALENIRILR+EKI+E+V+ ETAPYLQKR +EL
Sbjct: 305 DDVVEVLNEGGDFNHGFTYSGHPVAAAVALENIRILRDEKIVERVRTETAPYLQKRLREL 364

Query: 367 ADHPLVGEARG 377
           +DHPLVGE RG
Sbjct: 365 SDHPLVGEVRG 375


Lambda     K      H
   0.320    0.138    0.425 

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: 712
Number of extensions: 29
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: 456
Length of database: 400
Length adjustment: 32
Effective length of query: 424
Effective length of database: 368
Effective search space:   156032
Effective search space used:   156032
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources