GapMind for catabolism of small carbon sources

 

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

Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate 3610092 Dshi_3473 threonine dehydratase (RefSeq)

Query= SwissProt::P25306
         (595 letters)



>FitnessBrowser__Dino:3610092
          Length = 413

 Score =  181 bits (458), Expect = 7e-50
 Identities = 125/394 (31%), Positives = 195/394 (49%), Gaps = 9/394 (2%)

Query: 113 SPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSREELDKGVITASAGNHA 172
           +PL++   LS+R G   ++KRED   V S+K+RGA+N +S    E   +    ASAGNHA
Sbjct: 22  TPLQMNIHLSERYGAEIWLKREDLSPVRSYKIRGAFNAISKRVAEGQTQ-FACASAGNHA 80

Query: 173 QGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGG---DVVLYGKTFDEAQTHALELSEK 229
           QGVA A Q       I MP TTP+ KID  R  GG   D+ L G  FD+    A     +
Sbjct: 81  QGVAYACQHFGVHGVIFMPVTTPRQKIDKTRIFGGTAIDIELVGDYFDDTLAAAQRYCTE 140

Query: 230 DGLKYIPPFDDPGVIKGQGTIGTEINRQLKDI-HAVFIPVGGGGLIAGVATFFKQIAPNT 288
               ++ PFDD  VI+GQ T+  E+  QL+     V +PVGGGGL +G+  +F+      
Sbjct: 141 ASATFLSPFDDADVIEGQSTVAVELLEQLEGPPDMVILPVGGGGLSSGMKRYFEVCGVQV 200

Query: 289 KIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYTFAKCQELIDGMVLVA- 347
            +  VEP GA S+  +L  G    LS VD F DG AVA +G   F   +++    VL A 
Sbjct: 201 DLRLVEPCGARSLAKALETGAPQTLSKVDNFVDGAAVARIGARPFEILRDVPPDHVLGAP 260

Query: 348 NDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIVAIASGANMDFSKLHK 407
            D I   + ++ +    +LE +GA+A+       +   I  + +V + SG N DF +L +
Sbjct: 261 EDRICHTMLEMLNVEGIVLEPAGALAVDVLDTLRD--SITGKRVVCVTSGGNFDFERLPE 318

Query: 408 VTELAGLGSGKEALLATFMVEQQGSFKTFVGLVG-SLNFTELTYRFTSERKNALILYRVN 466
           V E +   +G +      + ++ G+ K F+G +G   +     Y   S R    +L  + 
Sbjct: 319 VKERSLRYAGLKKYFILRLPQRPGALKEFLGFLGPDDDIARFEYLKKSARNFGSVLIGIE 378

Query: 467 VDKESDLEKMIEDMKSSNMTTLNLSHNELVVDHL 500
                  E++   + ++     +++ + L+ + L
Sbjct: 379 TKDAGAFEQLFARLDAAGFPFRDITEDALLAEFL 412


Lambda     K      H
   0.317    0.135    0.382 

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: 490
Number of extensions: 26
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: 595
Length of database: 413
Length adjustment: 34
Effective length of query: 561
Effective length of database: 379
Effective search space:   212619
Effective search space used:   212619
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 (21.7 bits)
S2: 52 (24.6 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