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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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