GapMind for catabolism of small carbon sources

 

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

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 3609962 Dshi_3343 aminotransferase class-III (RefSeq)

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



>FitnessBrowser__Dino:3609962
          Length = 413

 Score =  182 bits (462), Expect = 2e-50
 Identities = 132/428 (30%), Positives = 216/428 (50%), Gaps = 32/428 (7%)

Query: 6   ADLMARRTAAVPRGVGQIH--PIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKI 63
           +DL+ RR   +   V   +  P+     +   + D  GR ++D    +   + GH HP++
Sbjct: 2   SDLLKRRARLMGPNVPTFYDPPLHIVRGEGVWLWDAGGRRYLDCYNNVP--HVGHCHPRV 59

Query: 64  IAAVTEQLNKL-THTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKI 122
           + A+  Q   L THT +    +E  ++  E++   +      + LLV TGSEAV+ A+++
Sbjct: 60  VDAIARQARVLNTHTRY---LHEGVLDYIERLTGTMDNGL-DQALLVCTGSEAVDVALRM 115

Query: 123 ARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVP---YSAGMGLMPG---GIFRALYPNEL 176
           ARAATG+ G+IA    YHG T     L+ +  P   YS  + L+P    G   A +    
Sbjct: 116 ARAATGKTGLIATDNTYHGNTTAVAQLSTRRPPIGGYSDHVRLVPAPEPGTDGAAF---- 171

Query: 177 HGVSIDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGIL 236
            G  +  + A +E           +AA+I+ P+    G    P+ F++   A     G L
Sbjct: 172 -GAHVARAAAELE------TAGHGVAALIVCPIFANEGLPCLPRGFLEPAVAALRTRGGL 224

Query: 237 LIADEVQTGAGRTG-TFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPG-G 294
           LI+DEVQ G GR G  F+  + +G+A D+ T  KS+  G+P+AGV  + E M A     G
Sbjct: 225 LISDEVQPGFGRLGDVFWGYQALGIAPDVVTLGKSMGNGYPVAGVVARTEIMGAFREAFG 284

Query: 295 LGGTYAGSPIACAAALAVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYPVIGDVRALGA 354
              T+ GSP+A AAA+AV++V E+E L++  K VG   +  L+A+  ++P I  VR  G 
Sbjct: 285 YFNTFGGSPVAAAAAMAVLDVLEDEGLVENAKRVGRYTLERLQAL--RHPAIDGVRGYGL 342

Query: 355 MIAVELFENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKG 414
             A++L +   +  PN A  A V  +A+ + +++   G   ++L++  PL    E  D+ 
Sbjct: 343 AFALDLVDTDGA--PNTALAAAVTEEAKRRSVLINRIGRDMHILKIRPPLPFAPEHGDRL 400

Query: 415 LAILEECF 422
             +L+  F
Sbjct: 401 GDVLQAAF 408


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: 439
Number of extensions: 24
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: 425
Length of database: 413
Length adjustment: 32
Effective length of query: 393
Effective length of database: 381
Effective search space:   149733
Effective search space used:   149733
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