GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Escherichia coli BW25113

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 15866 b1748 succinylornithine transaminase, PLP-dependent (NCBI)

Query= reanno::pseudo6_N2E2:Pf6N2E2_4013
         (425 letters)



>FitnessBrowser__Keio:15866
          Length = 406

 Score =  214 bits (544), Expect = 5e-60
 Identities = 142/399 (35%), Positives = 208/399 (52%), Gaps = 38/399 (9%)

Query: 25  PIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAY 84
           P      + + + D +G+E+IDFAGGIAV   GH HP++  A+ EQ +K  HT       
Sbjct: 22  PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTG-NGYTN 80

Query: 85  EPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARA------ATGRAGVIAFTGA 138
           EP + L +K+   +   FA +     +G+EA E A+K+AR        + ++G++AF  A
Sbjct: 81  EPVLRLAKKL---IDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNA 137

Query: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS--IDDSIASIERIFKNDA 196
           +HGRT+ T+   G+   YS     +P  I  A Y N+++  S  IDDS            
Sbjct: 138 FHGRTLFTVSAGGQPA-YSQDFAPLPADIRHAAY-NDINSASALIDDSTC---------- 185

Query: 197 EPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAME 256
                 A+I+EP+QGEGG   A   F++ LR LC++H  LLI DEVQTG GRTG  +A  
Sbjct: 186 ------AVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYM 239

Query: 257 QMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVF 316
             GV  DL T AK++ GGFP+  +    E    +  G  G TY G+P+A A A  V+E+ 
Sbjct: 240 HYGVTPDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELI 299

Query: 317 EEEHLLDRCKAVGERLVAGLKAIQKKYPVIGDVRALGAMIAVELFENGDSHKPNAAAVAQ 376
               +L+  K   +  V  L  I  +Y +  +VR LG +I   L  N D +   A  ++Q
Sbjct: 300 NTPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVL--NAD-YAGQAKQISQ 356

Query: 377 VVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGL 415
             AKA   G+++L  G  GNV+R    L   +E++  GL
Sbjct: 357 EAAKA---GVMVLIAG--GNVVRFAPALNVSEEEVTTGL 390


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: 443
Number of extensions: 18
Number of successful extensions: 4
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: 406
Length adjustment: 31
Effective length of query: 394
Effective length of database: 375
Effective search space:   147750
Effective search space used:   147750
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: 50 (23.9 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