GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astC in Herbaspirillum seropedicae SmR1

Align Succinylornithine transaminase; SOAT; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized)
to candidate HSERO_RS16670 HSERO_RS16670 acetylornithine aminotransferase

Query= curated2:Q3Z295
         (406 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS16670 HSERO_RS16670
           acetylornithine aminotransferase
          Length = 400

 Score =  292 bits (747), Expect = 1e-83
 Identities = 162/362 (44%), Positives = 218/362 (60%), Gaps = 5/362 (1%)

Query: 28  GEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNEPVLRLA 87
           G G  L D  GK Y+D+  G AVN LGHA   + +AL  Q+ K  +    + NEP + LA
Sbjct: 25  GHGMWLTDHNGKRYLDYLQGWAVNTLGHAPQCIADALAAQSKKLINPSPAFYNEPSIELA 84

Query: 88  KKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRY---GSHKSGIVAFKNAFHGRTLF 144
           K L   +  DRVFF NSG EANE A+KLARK+        GS +  I+ FK++FHGRTL 
Sbjct: 85  KLLTANSVFDRVFFANSGGEANEGAIKLARKWGKKNPAADGSARFEIITFKHSFHGRTLA 144

Query: 145 TVSAGGQPAYSQDFAPLPPDIRHAAYNDINSASALIDDATCAVIVEPIQGEGGVVPASNA 204
           T+SA G+  +   FAP  P    A  ND+ S  ALI + T AV++EP+QGEGGV+PAS  
Sbjct: 145 TMSASGKDGWDTMFAPQVPGFPKAVLNDLESVKALIGEHTVAVMLEPVQGEGGVIPASKE 204

Query: 205 FLQGLRELCDRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTTAKALGGGFPVGALL 264
           F+QGLR L    N LLI DEVQ+G+GRTG+L+AY H G+ PD++T AK +GGG P+ ALL
Sbjct: 205 FMQGLRSLTKEKNLLLIVDEVQSGMGRTGQLFAYQHSGIEPDIMTLAKGIGGGVPLAALL 264

Query: 265 TTEECASVMTVGTHGTTYGGNPLASAVAGKVLELINTPEMLNGVKQRHDWFVERLNTINH 324
             EE A     G  G TY GNPL +AV   V++ +  P  +  V++R  +  +R   I+ 
Sbjct: 265 AREEIA-CFEAGEQGGTYNGNPLMTAVGVAVIKELLKPGFMESVRERGQYLRQRSLEISE 323

Query: 325 RYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVMVLIAGGNVVRFAPALNVSEE 384
           +YG F   RG GLL    L  D   Q  + ++     G+++     N++RF PALNV++E
Sbjct: 324 KYG-FEGERGEGLLRALQLGRDIGPQIVEAARNLEPVGLLLNSPRPNLLRFMPALNVTKE 382

Query: 385 EV 386
           E+
Sbjct: 383 EI 384


Lambda     K      H
   0.319    0.136    0.408 

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: 432
Number of extensions: 22
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: 406
Length of database: 400
Length adjustment: 31
Effective length of query: 375
Effective length of database: 369
Effective search space:   138375
Effective search space used:   138375
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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