GapMind for catabolism of small carbon sources

 

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

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate 3607384 Dshi_0798 acetylornithine and succinylornithine aminotransferase (RefSeq)

Query= BRENDA::Q0K2K2
         (423 letters)



>lcl|FitnessBrowser__Dino:3607384 Dshi_0798 acetylornithine and
           succinylornithine aminotransferase (RefSeq)
          Length = 393

 Score =  207 bits (527), Expect = 5e-58
 Identities = 153/405 (37%), Positives = 201/405 (49%), Gaps = 48/405 (11%)

Query: 30  RAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTA--YQIVPYQGY 87
           + E A L + +GR + D  AGIAV   GH HPR++ A+  Q +   H +  YQI   Q  
Sbjct: 18  KGEGAWLIEADGRRFLDLGAGIAVNALGHAHPRLVAALTDQAQALWHVSNLYQIPAQQ-- 75

Query: 88  VTLAERINALVPIQGLNKTALFT-TGAEAVENAIKIARAH---TGRPG---VIAFSGAFH 140
             LAE + A    +    T  FT +G E+ E A+K+ R H    G+P    ++ F G+FH
Sbjct: 76  -KLAEMLVA----ETFADTVFFTNSGTESCELAVKMVRKHFHDAGQPERVEILTFEGSFH 130

Query: 141 GRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDIDPAR 200
           GR+  G+A  G     K GFGP      H PF           ALQ+            R
Sbjct: 131 GRSSAGIAAAGSEKMTK-GFGPLLPGFRHLPF-------GNHEALQSAVN--------DR 174

Query: 201 VAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHHDV 260
            AAI+VEPVQGEGG +A P   ++GLR +CDQHGI++I DEVQ G GRTG++FA     V
Sbjct: 175 TAAIMVEPVQGEGGIRALPDACLKGLRDLCDQHGILMILDEVQCGVGRTGRLFAHEWAGV 234

Query: 261 EPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIEEEK 320
            PD++ +AK + GG PL AV   A        G  G TY GNPL  A   AV++ +  + 
Sbjct: 235 SPDIMMVAKGIGGGFPLGAVLATADAASGMTAGTHGSTYGGNPLGCAVGCAVLETVCADG 294

Query: 321 LCE---RSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQPSAEHAKRVQ 377
             E   R A L +Q  E L+A+       AEVRG G M+      P T    A +     
Sbjct: 295 FLEEVRRKAGLMRQALEGLVAE--FPGVFAEVRGAGLMLGLVCRAPNTDVVQAGY----- 347

Query: 378 TRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALA 422
                 G  +L      NV+R L PLTI  A+   ALA L +A A
Sbjct: 348 ------GAEVLVVPAAENVVRLLPPLTITDAEIREALARLRKAAA 386


Lambda     K      H
   0.321    0.136    0.400 

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: 459
Number of extensions: 29
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: 423
Length of database: 393
Length adjustment: 31
Effective length of query: 392
Effective length of database: 362
Effective search space:   141904
Effective search space used:   141904
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 (21.9 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 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