GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocD in Klebsiella michiganensis M5al

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate BWI76_RS11670 BWI76_RS11670 aspartate aminotransferase family protein

Query= curated2:Q89RB7
         (404 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS11670 BWI76_RS11670 aspartate
           aminotransferase family protein
          Length = 406

 Score =  233 bits (593), Expect = 1e-65
 Identities = 130/379 (34%), Positives = 203/379 (53%), Gaps = 6/379 (1%)

Query: 20  YEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSRA 79
           Y P   +  RGEG  +WD  G  Y+D     +  + GH HP+++ A+ EQA +   T   
Sbjct: 18  YAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTGNG 77

Query: 80  FHNDQLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVCA 139
           + N+ +    +++   T + +V   NSGAEA E+A+K  RK+ ++  G   +++ I+   
Sbjct: 78  YTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFG--SEKSGIVAFK 135

Query: 140 DNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQGE 199
           + FHGRTL  V     P     F P  P  +   + D  + +  I  NT A +VEP+QGE
Sbjct: 136 NAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDDNTCAVIVEPMQGE 195

Query: 200 AGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKALA 259
            GV+   A +   +RELC A+N +L+ DE+QTG+GRTG+L A  H G+  D+    KAL 
Sbjct: 196 GGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKALG 255

Query: 260 GGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGAR 319
           GGF P+ A+L++      +  G HG+T+GGNPLACAVA      +    ++    ++   
Sbjct: 256 GGF-PIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVKQRHQW 314

Query: 320 LLEGLKDIRA--NTVREVRGRGLMLAVELHPE-AGRARRYCEALQGKGILAKDTHGHTIR 376
             E L  I A     +E+RG GL++   L  E AG+A+        +G++      + +R
Sbjct: 315 FCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLMILIAGANVVR 374

Query: 377 IAPPLVITSDEVDWALEQF 395
            AP L+I+ DEV+  L++F
Sbjct: 375 FAPALIISEDEVNSGLDRF 393


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: 403
Number of extensions: 21
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: 404
Length of database: 406
Length adjustment: 31
Effective length of query: 373
Effective length of database: 375
Effective search space:   139875
Effective search space used:   139875
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