GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocD in Pseudomonas fluorescens FW300-N2C3

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate AO356_17010 AO356_17010 acetylornithine aminotransferase

Query= curated2:Q89RB7
         (404 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17010 AO356_17010
           acetylornithine aminotransferase
          Length = 391

 Score =  265 bits (678), Expect = 1e-75
 Identities = 157/388 (40%), Positives = 218/388 (56%), Gaps = 13/388 (3%)

Query: 20  YEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSRA 79
           Y+P+ +  + G G  +WD DG  YLD ++  +  + GH HP+++AA+ EQA  L  TS  
Sbjct: 10  YQPLALNFTHGLGTRLWDQDGREYLDAVAGVAVTNVGHSHPRLVAAISEQAGLLLHTSNL 69

Query: 80  FHNDQLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVCA 139
           +  D      +++  L+G  +    NSGAEA E+A+K  R +G+  KG+  +Q  ++V  
Sbjct: 70  YSIDWQQRLAQKLTQLSGMERAFFNNSGAEANETALKLARLYGWH-KGI--EQPLVVVMD 126

Query: 140 DNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQ---AITPNTVAFLVEPI 196
           + FHGRTLG +  S  P  R  +      F  +PFGD AALEQ   A     VA LVEPI
Sbjct: 127 NAFHGRTLGTMSASDGPSVRLGYNRLPGDFIKVPFGDLAALEQIQQAHAERIVAVLVEPI 186

Query: 197 QGEAGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGK 256
           QGE+GV + P GY   +R+LC+    +L+LDEIQTG+GRTG+  A QHEGI  DV  L K
Sbjct: 187 QGESGVQLAPPGYLKALRQLCSRRAWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTLAK 246

Query: 257 ALAGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQ 316
            L  G  P+ A L+  +      PG HGSTFGGNPLAC V    + ++ E+ ++ NA  Q
Sbjct: 247 GLGNG-VPIGACLARGKAAELFTPGSHGSTFGGNPLACRVGCTVLDIIEEQALVGNARHQ 305

Query: 317 GARLLEGLKDIRAN--TVREVRGRGLMLAVEL-HPEAGRARRYCEALQGKGILAKDTHGH 373
           G +LL  L+   A    V  +RG+GLM+ +EL  P      R   A +  G+L   T G 
Sbjct: 306 GEQLLSRLRTELAENPNVLAIRGQGLMIGIELKQPVRDLTLR---AARDHGLLINVTRGQ 362

Query: 374 TIRIAPPLVITSDEVDWALEQFATTLTQ 401
           TIR+ PPL I   EV+  +   +  L Q
Sbjct: 363 TIRLLPPLTIDGREVEMIVRGVSRCLAQ 390


Lambda     K      H
   0.319    0.136    0.405 

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: 457
Number of extensions: 20
Number of successful extensions: 6
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: 404
Length of database: 391
Length adjustment: 31
Effective length of query: 373
Effective length of database: 360
Effective search space:   134280
Effective search space used:   134280
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 (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 paper from 2022 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