GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Alicycliphilus denitrificans K601

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_013518270.1 ALIDE2_RS17550 aspartate aminotransferase family protein

Query= curated2:Q89RB7
         (404 letters)



>NCBI__GCF_000204645.1:WP_013518270.1
          Length = 398

 Score =  249 bits (637), Expect = 8e-71
 Identities = 159/394 (40%), Positives = 219/394 (55%), Gaps = 20/394 (5%)

Query: 18  HNYEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTS 77
           + Y  + + L RG+GV VWD +G +YLD L   +  + GH HP+++ A+ EQ  +L  TS
Sbjct: 14  NTYGRVPIALERGQGVRVWDVNGKQYLDGLGGIAVNTLGHNHPRLVPALQEQIAKLIHTS 73

Query: 78  RAFHNDQLAPFYEEIAAL-TGSHKVLPM---NSGAEAVESAIKSVRKWGYEVKGVPDDQA 133
             +H     P  EE+A L TG  ++      N+G EA E AIK  RK+G + KG+  ++ 
Sbjct: 74  NYYH----VPGQEELARLLTGRARMTNAFFCNTGLEANECAIKIARKYGVD-KGI--EKP 126

Query: 134 EIIVCADNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAI--TPNTVAF 191
           EI+V    FHGR++  +  + +P+ R  FGP   GF  +   D  AL++A    PN VA 
Sbjct: 127 EIVVYDHAFHGRSIATMTATGNPKVRNGFGPLLEGFIRVAPNDIEALQEATEGNPNVVAV 186

Query: 192 LVEPIQGEAGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADV 251
           L+EPIQGE G+      Y  +VR+LC AN  +L+LDE+Q G+GRTGK  A Q  GI  DV
Sbjct: 187 LMEPIQGEGGLHPMRVEYLQQVRKLCDANGWLLMLDEVQAGMGRTGKWFAHQWAGIVPDV 246

Query: 252 TLLGKALAGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIE 311
             L K L  G  PV AVL++      L+PG HGSTFGGNPLA       +R++ EEG+++
Sbjct: 247 MTLAKGLGSG-VPVGAVLAHGAASEVLKPGNHGSTFGGNPLAMRAGVETIRIMEEEGLLQ 305

Query: 312 NAARQGARLLEGLKDIRANT--VREVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKD 369
           NAA  GA L  GL+    +   V EVRG+GL++ VEL    G      +     G+L   
Sbjct: 306 NAADVGAHLKAGLQQALGSVPGVNEVRGQGLIIGVELDRPCG---VLIDRAAQAGLLLSV 362

Query: 370 THGHTIRIAPPLVITSDEVDWALEQFATTLTQDF 403
           T    IR+ P L +T  E D  +    T L Q F
Sbjct: 363 TADRVIRLVPALTLTRAEAD-EIVALLTPLVQAF 395


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: 469
Number of extensions: 27
Number of successful extensions: 7
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: 398
Length adjustment: 31
Effective length of query: 373
Effective length of database: 367
Effective search space:   136891
Effective search space used:   136891
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 Apr 09 2024. 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