GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Dinoroseobacter shibae DFL-12

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate 3607958 Dshi_1366 aminotransferase class-III (RefSeq)

Query= BRENDA::Q9I6J2
         (456 letters)



>FitnessBrowser__Dino:3607958
          Length = 441

 Score =  271 bits (694), Expect = 2e-77
 Identities = 152/426 (35%), Positives = 233/426 (54%), Gaps = 22/426 (5%)

Query: 24  PFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMR 83
           PFT  +Q  +   R+   A+G+Y   +EG ++LD  AGLWC N G+ R  +V+A   Q  
Sbjct: 18  PFTANRQF-KSNPRMFVAADGMYYTTAEGRQVLDGTAGLWCCNAGHKRPRIVEAIQAQAA 76

Query: 84  ELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQ 143
           EL  Y   FQ  HP   ELA  + ++AP+GM+HVF+T SGSEA ++ L++   Y   +G+
Sbjct: 77  ELD-YAPAFQMGHPRAFELANRLVEIAPDGMDHVFYTNSGSEAVESALKIALAYHRARGE 135

Query: 144 PQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDMSPDEF 203
             +  +IGR  GYHG    G+S+GG+    +     + G+ H+   +           E 
Sbjct: 136 AGRTRLIGRERGYHGVNFGGISVGGIVNNRKHFGTLLTGVDHLPHTHIPENQWSRGMPEL 195

Query: 204 GVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFIADE 263
           G   A+ LE+ I   G E +AA I EP+ G+ GV++PP  Y  ++R+I   + I+ I DE
Sbjct: 196 GAHLADDLERIIALHGAETIAAVIVEPMAGSTGVLLPPKGYLQRLRKITQDHGIVLIFDE 255

Query: 264 VICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGG----EF 319
           VI GFGR G  FG+Q +G  PD++  AKGLT+G IPMG V+    I +   QG     E 
Sbjct: 256 VITGFGRVGAAFGAQRFGVTPDMITCAKGLTNGVIPMGAVLCGSHIHDAFMQGPENLIEL 315

Query: 320 YHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEARGVG 379
           +HG+TYSG+P+A+A  L  +   RE+ +  +   +  PY Q+    L     V + R +G
Sbjct: 316 FHGYTYSGNPIASAAGLATLETYREDDLFARA-LDLEPYWQEALHSLKGARHVIDIRNLG 374

Query: 380 MVAALELV-----KNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDPS 434
           ++ A+EL        K+  + F D           +  G+++R  GD + +SPPL+I+ +
Sbjct: 375 LIGAIELEPISGHPTKRAFQAFLD----------AYDKGVLIRTTGDIIALSPPLIIETA 424

Query: 435 QIDELI 440
           QID ++
Sbjct: 425 QIDRIV 430


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: 570
Number of extensions: 34
Number of successful extensions: 6
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: 441
Length adjustment: 33
Effective length of query: 423
Effective length of database: 408
Effective search space:   172584
Effective search space used:   172584
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