GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3607384
          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:

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