GapMind for catabolism of small carbon sources

 

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

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate AO356_28705 AO356_28705 hypothetical protein

Query= BRENDA::Q9I6J2
         (456 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28705
          Length = 449

 Score =  293 bits (750), Expect = 8e-84
 Identities = 166/418 (39%), Positives = 235/418 (56%), Gaps = 13/418 (3%)

Query: 24  PFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMR 83
           P +     N     II + +G YI D EG+++LD + GLW VNVG+ R  +  A   Q+ 
Sbjct: 15  PMSSSAPANRSKTLIIARGDGNYITDIEGHRMLDGVGGLWNVNVGHNRPSVKAAIAAQLD 74

Query: 84  ELPFYNLFFQTAHPPVVELAKAIADV-APEGMNHVFFTGSGSEANDTVLRMVRHYWATKG 142
           EL +Y  F   AHP V +LA+ +  + A E M  V F+  GS+A +T L+M R YW   G
Sbjct: 75  ELAYYQTFDGIAHPRVFDLAERLTSMFAQENMARVLFSSGGSDAVETALKMARQYWIASG 134

Query: 143 QPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDM-SPD 201
           +P +   +   NGYHG  V G S+GG    H      + G   +  P+ Y    D   P+
Sbjct: 135 EPGRTRFLSLRNGYHGVHVGGTSVGGNGVYHYNHGPLLAGCHLLDTPWLYRNPWDCRDPE 194

Query: 202 EFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFIA 261
           E       QLE +I  +G + +AA IAEP+QGAGGVIVPP  YW ++RE+  ++ IL IA
Sbjct: 195 ELTAHCIRQLEDQIALLGPQTIAALIAEPVQGAGGVIVPPAHYWKRLREVCDRHGILLIA 254

Query: 262 DEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGGEF-- 319
           DEV+ GFGRTG   GS+ +G APD++ +AKG+T+GYIPMG  V    I + +  G  F  
Sbjct: 255 DEVVTGFGRTGCMLGSRGWGVAPDVLCLAKGITAGYIPMGATVFNQRIADAIENGPGFSS 314

Query: 320 --YHGFTYSGHPVAAAVALENIRILREEKI---IEKVKAETAPYLQKRWQELADHPLVGE 374
              HG+TYSGHP A A AL  + I+  E +     KV A+    LQ   +  A   +VGE
Sbjct: 315 VIMHGYTYSGHPTACAAALAVLDIVEAEDLPGNAGKVGAQLLEQLQPLTERYA---VVGE 371

Query: 375 ARGVGMVAALELVKNKKTRERFTD-KGVGMLCREHCFRNGLIMRAVGDTMIISPPLVI 431
            RG G++ A++LV +K TRE      G+     E   R G+++R +G+ +++SPPL +
Sbjct: 372 VRGKGLMIAVDLVADKVTREPLDPANGLASRIAEQARRAGVLVRPIGNKIVMSPPLTL 429


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: 562
Number of extensions: 25
Number of successful extensions: 5
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: 449
Length adjustment: 33
Effective length of query: 423
Effective length of database: 416
Effective search space:   175968
Effective search space used:   175968
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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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