GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__ANA3:7025958
          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:

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