GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabT in Dinoroseobacter shibae DFL-12

Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate 3608039 Dshi_1446 aminotransferase class-III (RefSeq)

Query= SwissProt::Q84P52
         (520 letters)



>lcl|FitnessBrowser__Dino:3608039 Dshi_1446 aminotransferase
           class-III (RefSeq)
          Length = 444

 Score =  240 bits (612), Expect = 9e-68
 Identities = 140/422 (33%), Positives = 222/422 (52%), Gaps = 15/422 (3%)

Query: 92  GSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATKQLNELAFYHSFWNRSTKPSLDLA 151
           G Y+ D +GK+YLD   G   + LG + P + AA   Q++++AF H+ +   T    ++ 
Sbjct: 21  GCYIIDADGKRYLDGSGGAAVSCLGHDHPAVRAALHAQIDKIAFAHTGF--FTSEPAEVL 78

Query: 152 KELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNNALGRPDKKKFIARTKSYHGSTLI 211
            + L       + K +  + GSE+ +  +KL   +    G P + + IAR +SYHG+TL 
Sbjct: 79  CDALIAAAPKGIEKVYLLSGGSESVEAALKLARQFFLETGEPRRHRVIARRQSYHGNTLG 138

Query: 212 SASLSGLPALHQQFDLPAPFVLHTDCPHFWRFHQPGETEEEFSTRLANNLENLILKEGPE 271
           + +  G     +++        H D  + +R    GE++  +  R A+ L   I + GPE
Sbjct: 139 ALAAGGNAWRREKYAPLLVETYHIDPCYAYRHQAVGESDAAYGRRAADALRTEIERLGPE 198

Query: 272 TIAAFIAEPVMGA-GGVIPPPATYFEKVQAILKKYDILFIADEVICGFGRLGTMFGCEKY 330
           T+ AFIAEPV+GA  G +PP   YFE+++ I  +Y +L I DEV+CG GR GT+F CE+ 
Sbjct: 199 TVMAFIAEPVVGATAGAVPPAPGYFERIREICDEYGVLLILDEVMCGMGRTGTLFACEQD 258

Query: 331 NIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSNKLGTFSHGFTYSGHPVSCAVAL 390
            I PD+V++AK L +GY PIGA+L S  + D I   S   G+F HG TY GHP++ A A 
Sbjct: 259 GISPDIVTIAKGLGAGYAPIGAMLASGRIYDAIAQGS---GSFQHGHTYHGHPLAAAAAG 315

Query: 391 ETLKIYKERNIIEQVNRISPKFQEGLK-AFSDSPIIGEIRGTGLLHGTEFTDNKSPNDPF 449
             ++  +    + QV       Q  L+ A      +G+IRG GL  G E  +++    P 
Sbjct: 316 AVVETLRAPGTMAQVRAKGATLQSRLEAALGQHSHVGDIRGRGLFRGIELVEDRDTKRPL 375

Query: 450 PPEWGIGAYFGARCEKHGVLVRVA--------GDNIMMSPPYILSLEEIDELIIKYGKAL 501
            P   + A   A     G++            GD+I+++PP+I+  ++ID L+    +A+
Sbjct: 376 DPARKVSARIKAAAMARGLICYPGSGTIDGKHGDHILLAPPFIIEDKQIDALVHMLAEAI 435

Query: 502 KD 503
            D
Sbjct: 436 DD 437


Lambda     K      H
   0.317    0.135    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: 531
Number of extensions: 23
Number of successful extensions: 7
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: 520
Length of database: 444
Length adjustment: 34
Effective length of query: 486
Effective length of database: 410
Effective search space:   199260
Effective search space used:   199260
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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 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