Alignments for a candidate for patA in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for patA in Pseudomonas fluorescens FW300-N2C3

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate AO356_27230 AO356_27230 hypothetical protein

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27230
          Length = 871

 Score =  264 bits (675), Expect = 8e-75
 Identities = 173/433 (39%), Positives = 239/433 (55%), Gaps = 37/433 (8%)

Query: 39  IEYFKEHVNPGFLEYRKSVTAGGDYGAVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGH 98
           I  F++HVNP   E  + V  G D   V    G    L D QG+ ++D LG +G    GH
Sbjct: 7   ISPFEQHVNPAVGELIRRV--GLDKTFVR---GEGCYLYDAQGRAYLDFLGAYGALPFGH 61

Query: 99  RNPVVVSAVQN-QLAKQPLHSQELLDPLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAA 157
               +++ + + QL+++P+  Q        +LA+ L A+ PG  +   F NSG E+VEAA
Sbjct: 62  SPDALLAELASFQLSREPIFVQPSSLAASGLLAQRLLAIAPGDYRSVTFQNSGAETVEAA 121

Query: 158 LKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEA 217
           LK   A     G+   ++T  +FHGK+LGALSAT    +++ F   LPGF  V +G+I+A
Sbjct: 122 LK---ACLIKTGRKRILSTHQSFHGKTLGALSATGSDKYQEGFQAPLPGFDFVDYGDIQA 178

Query: 218 MRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGM 277
           +   L   ++  D  AAVI+EP+QGEGG+ LPPP YL  +R  CD  G L+I+DEVQTG+
Sbjct: 179 LEDQL---QRHPDAYAAVIIEPVQGEGGINLPPPEYLQQIRAACDRSGTLLIIDEVQTGL 235

Query: 278 GRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNP 337
           GRTG+MFA     VQ D L LAKALGGGVMPIGA + ++  +S  F N   H++TFGGN 
Sbjct: 236 GRTGQMFA--SAGVQADCLLLAKALGGGVMPIGACLISKNAYSEDFQNK--HSSTFGGNT 291

Query: 338 LACAAALATINVLLE-QNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFV 396
           LAC   L  +++L E Q+L       G  LL+   +LA  +   ++E RG G L+ IEF 
Sbjct: 292 LACRIGLKVLDLLDERQDLLDSVRDNGRYLLEQLNELAARHASFIKEVRGAGYLIGIEFD 351

Query: 397 DNEIGY-----NFASEMFRQR---------------VLVAGTLNNAKTIRIEPPLTLTIE 436
            +   Y      F   M  Q                V VA TLN A  +R+EPPL     
Sbjct: 352 LDRSHYPQFYGGFTGIMGEQESLVPILASYLLNVEGVRVAPTLNGANVMRVEPPLIAGRA 411

Query: 437 QCELVIKAARKAL 449
           +CE+ I+A  + L
Sbjct: 412 ECEVFIQALARTL 424


Lambda     K      H
   0.320    0.135    0.393 

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: 868
Number of extensions: 41
Number of successful extensions: 8
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: 459
Length of database: 871
Length adjustment: 38
Effective length of query: 421
Effective length of database: 833
Effective search space:   350693
Effective search space used:   350693
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: 54 (25.4 bits)

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

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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, 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

GapMind for catabolism of small carbon sources