GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Phaeobacter inhibens BS107

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate GFF919 PGA1_c09350 aminotransferase class-III

Query= BRENDA::Q9I6J2
         (456 letters)



>lcl|FitnessBrowser__Phaeo:GFF919 PGA1_c09350 aminotransferase
           class-III
          Length = 450

 Score =  321 bits (822), Expect = 3e-92
 Identities = 172/419 (41%), Positives = 251/419 (59%), Gaps = 10/419 (2%)

Query: 39  ITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMRELPFYNLFFQTAHPP 98
           + + EG+Y++DS+G K ++ +AGLWC ++GY   E++ A T Q+ +LPF + F    H P
Sbjct: 19  LERGEGIYVFDSDGRKYIEGLAGLWCTSLGYSNTEVMDAITEQLHKLPFTHTFGGKTHQP 78

Query: 99  VVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYHG 158
           + +LA  +A + P    ++FF  SGS+ANDT  +M+R+Y+   G+P+K+ +I R  GYHG
Sbjct: 79  IQDLADKLAAMVPVEDAYIFFGNSGSDANDTHYKMLRYYFNAIGKPEKRKIITRERGYHG 138

Query: 159 STVAGVSLGGMKALHEQGDFPIP--GIVHIAQPYWY-GEGGDMSPDEFGVWAAEQLEKKI 215
            TVA  SL  + A     D P+    I+    P++Y    G+ +  +F     + LE +I
Sbjct: 139 VTVAAGSLTSLPANLAHFDAPLEALSILRADSPHYYTARQGNETEAQFVERILQNLEDQI 198

Query: 216 LEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFIADEVICGFGRTGEWF 275
           +    + +AA I EPI GA GVIVPPD Y+  ++ +L KY IL  ADEVICGFGRTG  F
Sbjct: 199 ISEDPDTIAAMIVEPITGASGVIVPPDGYYEGLQALLRKYGILIWADEVICGFGRTGADF 258

Query: 276 GSQYYGNAPDLMPIAKGLTSGYIPMGGVVV----RDEIVEVLNQGGEFYHGFTYSGHPVA 331
           G    G  PDLM  AK L+S Y P+   V+     + +V+  N+ G F HG+TYSGHP A
Sbjct: 259 GCTTMGITPDLMTFAKQLSSAYFPISASVIPGWMYEAMVDQTNEVGVFGHGYTYSGHPAA 318

Query: 332 AAVALENIRILREEKIIEKVKAETAPYLQKRWQEL-ADHPLVGEARGVGMVAALELVKNK 390
            A AL+ + I   + + +   AE   YLQ + +E+  DHPLVGE RG G++AALELV NK
Sbjct: 319 CAAALKTLEIYERDNLFDHA-AEVGSYLQTQLREIFTDHPLVGEVRGKGLIAALELVSNK 377

Query: 391 KTRERFTDKGVGMLCREHCFRNGLIMRAV-GDTMIISPPLVIDPSQIDELITLARKCLD 448
            T   F     G   +  C  NGLI+RAV G+ + + PPL+I   ++D+++T  +  +D
Sbjct: 378 TTGASFDKGRAGATAQRLCQDNGLILRAVAGNAVALCPPLIITREEVDDMLTRLKTAID 436


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: 555
Number of extensions: 22
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: 450
Length adjustment: 33
Effective length of query: 423
Effective length of database: 417
Effective search space:   176391
Effective search space used:   176391
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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