GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Shewanella sp. ANA-3

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate 7025958 Shewana3_3106 beta alanine--pyruvate transaminase (RefSeq)

Query= BRENDA::Q9I6J2
         (456 letters)



>lcl|FitnessBrowser__ANA3:7025958 Shewana3_3106 beta
           alanine--pyruvate transaminase (RefSeq)
          Length = 446

 Score =  307 bits (786), Expect = 5e-88
 Identities = 177/433 (40%), Positives = 247/433 (57%), Gaps = 20/433 (4%)

Query: 17  SRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQ 76
           S +H+  PFT  +Q  +   R++ +AEG+Y  D  GNK+LD+ AGLWC N G+GR E+ +
Sbjct: 14  SLEHYWMPFTANRQF-KASPRLLAQAEGMYYTDINGNKVLDSTAGLWCCNAGHGRREISE 72

Query: 77  AATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRH 136
           A ++Q+RE+  Y   FQ  HP   ELA+ + +++PEG+N VFFT SGSE+ DT L+M   
Sbjct: 73  AVSKQIREMD-YAPSFQMGHPLAFELAERLTELSPEGLNKVFFTNSGSESVDTALKMALC 131

Query: 137 YWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGM----KALHEQGDFPIPGIVHIAQPYWY 192
           Y    GQ  +   IGR  GYHG    G+S+GG+    KA   Q    + G+ H+      
Sbjct: 132 YHRANGQASRTRFIGRELGYHGVGFGGISVGGLSNNRKAFSGQ---LLQGVDHLPHTLDI 188

Query: 193 GEGG-DMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREI 251
                       G   AE LE+ +   G EN+AA I EP+ G+ GVI+PP  Y  ++REI
Sbjct: 189 QNSAFSRGLPSLGAEKAEVLEQLVTLHGAENIAAVIVEPMSGSAGVILPPQGYLKRLREI 248

Query: 252 LAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVE 311
             KY IL I DEVI  FGR G  F SQ +G  PD++  AK + +G IPMG V V+D I +
Sbjct: 249 TQKYGILLIFDEVITAFGRVGAAFASQRWGVIPDIITTAKAINNGAIPMGAVFVQDFIHD 308

Query: 312 VLNQGG----EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELA 367
              QG     EF+HG+TYSGHPVAAA AL  + I   E++ E+   E   Y +     L 
Sbjct: 309 TCMQGPTELIEFFHGYTYSGHPVAAAAALATLSIYENEQLFER-SFELERYFEDAVHSLK 367

Query: 368 DHPLVGEARGVGMVAALELVKNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMIISP 427
             P V + R  G+VA  +L  N +   +   +G  +   EHCF  G ++RA GD + ISP
Sbjct: 368 GLPNVIDIRNTGLVAGFQLAPNSQGAGK---RGYSVF--EHCFHQGTLVRATGDIIAISP 422

Query: 428 PLVIDPSQIDELI 440
           PL+++  QID+++
Sbjct: 423 PLIVEKHQIDQIV 435


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: 538
Number of extensions: 21
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: 446
Length adjustment: 33
Effective length of query: 423
Effective length of database: 413
Effective search space:   174699
Effective search space used:   174699
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 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