GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davT in Phaeobacter inhibens BS107

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate GFF919 PGA1_c09350 aminotransferase class-III

Query= reanno::pseudo3_N2E3:AO353_11510
         (425 letters)



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

 Score =  169 bits (429), Expect = 1e-46
 Identities = 133/407 (32%), Positives = 205/407 (50%), Gaps = 38/407 (9%)

Query: 36  VTDVEGREFIDFAGGIAVLNTGHLHPKVIAAVTEQLNKL--THTCFQVLAYEPYVELCEK 93
           V D +GR++I+   G+   + G+ + +V+ A+TEQL+KL  THT F    ++P  +L +K
Sbjct: 27  VFDSDGRKYIEGLAGLWCTSLGYSNTEVMDAITEQLHKLPFTHT-FGGKTHQPIQDLADK 85

Query: 94  INAKVPGDFAKKTLLVTTGSEAVENSIKIARAATGRAG------VIAFTGAYHGRTMMTL 147
           + A VP + A       +GS+A +   K+ R      G      +I     YHG T+   
Sbjct: 86  LAAMVPVEDAY-IFFGNSGSDANDTHYKMLRYYFNAIGKPEKRKIITRERGYHGVTVAAG 144

Query: 148 GLTG---KVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIAS-IERIFKN------DAE 197
            LT     +  + A +  +   I RA  P+       +++ A  +ERI +N        +
Sbjct: 145 SLTSLPANLAHFDAPLEAL--SILRADSPHYYTARQGNETEAQFVERILQNLEDQIISED 202

Query: 198 PRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQ 257
           P  IAA+I+EP+ G  G  V P  + + L+AL  ++GIL+ ADEV  G GRTG  F    
Sbjct: 203 PDTIAAMIVEPITGASGVIVPPDGYYEGLQALLRKYGILIWADEVICGFGRTGADFGCTT 262

Query: 258 MGVAADLTTFAKSIAGG-FPLAGVC-------GKAEYMDAIAPGGLGGTYAGSPIACAAA 309
           MG+  DL TFAK ++   FP++             +  + +   G G TY+G P ACAAA
Sbjct: 263 MGITPDLMTFAKQLSSAYFPISASVIPGWMYEAMVDQTNEVGVFGHGYTYSGHPAACAAA 322

Query: 310 LAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFEN----GD 365
           L  +E++E ++L D    VG  L T L+ I   +P++GEVR  G + A+EL  N      
Sbjct: 323 LKTLEIYERDNLFDHAAEVGSYLQTQLREIFTDHPLVGEVRGKGLIAALELVSNKTTGAS 382

Query: 366 SHKPNAAAVAKVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLD 412
             K  A A A+ +   +D GLIL +    GN + +  PL    E++D
Sbjct: 383 FDKGRAGATAQRL--CQDNGLILRAVA--GNAVALCPPLIITREEVD 425


Lambda     K      H
   0.320    0.137    0.395 

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: 442
Number of extensions: 22
Number of successful extensions: 3
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: 425
Length of database: 450
Length adjustment: 32
Effective length of query: 393
Effective length of database: 418
Effective search space:   164274
Effective search space used:   164274
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