GapMind for catabolism of small carbon sources

 

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

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate 3608039 Dshi_1446 aminotransferase class-III (RefSeq)

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__Dino:3608039
          Length = 444

 Score =  198 bits (504), Expect = 2e-55
 Identities = 140/420 (33%), Positives = 206/420 (49%), Gaps = 31/420 (7%)

Query: 33  CRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLELCEI 92
           C + D +G+ YLD +GG AV   GH HP V AA+ AQ+ K++         EP   LC+ 
Sbjct: 22  CYIIDADGKRYLDGSGGAAVSCLGHDHPAVRAALHAQIDKIAFAHTGFFTSEPAEVLCDA 81

Query: 93  MNQKVPGDFAKKTLLVTTGSEAVENAVKIAR------AATKRSGTIAFSGAYHGRTHYTL 146
           +    P    +K  L++ GSE+VE A+K+AR         +R   IA   +YHG T   L
Sbjct: 82  LIAAAPKGI-EKVYLLSGGSESVEAALKLARQFFLETGEPRRHRVIARRQSYHGNTLGAL 140

Query: 147 ALTGKVNPYSAGMGLMPGHVYRALYPCPLH---GISEDDAI-----ASIHRIFKNDAAPE 198
           A  G          L+    +  + PC  +    + E DA      A   R       PE
Sbjct: 141 AAGGNAWRREKYAPLLVETYH--IDPCYAYRHQAVGESDAAYGRRAADALRTEIERLGPE 198

Query: 199 DIAAIVIEPVQGE-GGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQM 257
            + A + EPV G   G    +P + +R+R +CDE+G++LI DEV  G GRTGTLFA EQ 
Sbjct: 199 TVMAFIAEPVVGATAGAVPPAPGYFERIREICDEYGVLLILDEVMCGMGRTGTLFACEQD 258

Query: 258 GVAPDLTTFAKSIAGGF-PLAGVTGRAEVMDAVAPGG----LGGTYAGNPIACVAALEVL 312
           G++PD+ T AK +  G+ P+  +     + DA+A G      G TY G+P+A  AA  V+
Sbjct: 259 GISPDIVTIAKGLGAGYAPIGAMLASGRIYDAIAQGSGSFQHGHTYHGHPLAAAAAGAVV 318

Query: 313 KVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNK---PD 369
           +       + +    G  L+  L A   +H  +GD+RG G    IEL ED D  +   P 
Sbjct: 319 ETLRAPGTMAQVRAKGATLQSRLEAALGQHSHVGDIRGRGLFRGIELVEDRDTKRPLDPA 378

Query: 370 AKLTAEIVARARDKGLILLS-----CGPYYNVLRILVPLTIEDAQIRQGLEIISQCFDEA 424
            K++A I A A  +GLI         G + + + +  P  IED QI   + ++++  D+A
Sbjct: 379 RKVSARIKAAAMARGLICYPGSGTIDGKHGDHILLAPPFIIEDKQIDALVHMLAEAIDDA 438


Lambda     K      H
   0.320    0.137    0.401 

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: 530
Number of extensions: 33
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: 426
Length of database: 444
Length adjustment: 32
Effective length of query: 394
Effective length of database: 412
Effective search space:   162328
Effective search space used:   162328
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