GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Alicycliphilus denitrificans K601

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_013518270.1 ALIDE2_RS17550 aspartate aminotransferase family protein

Query= BRENDA::O30508
         (406 letters)



>NCBI__GCF_000204645.1:WP_013518270.1
          Length = 398

 Score =  269 bits (688), Expect = 9e-77
 Identities = 153/366 (41%), Positives = 215/366 (58%), Gaps = 11/366 (3%)

Query: 30  RGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHVSNVFTNEPALRL 89
           RG+G RVWD +G++ +D  GGIAV +LGH HP LV AL EQ  ++ H SN +       L
Sbjct: 25  RGQGVRVWDVNGKQYLDGLGGIAVNTLGHNHPRLVPALQEQIAKLIHTSNYYHVPGQEEL 84

Query: 90  ARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSFHGRTLFTV 149
           AR L         F  N+G EANE A K+AR+Y  D  G +K EI+   ++FHGR++ T+
Sbjct: 85  ARLLTGRARMTNAFFCNTGLEANECAIKIARKYGVDK-GIEKPEIVVYDHAFHGRSIATM 143

Query: 150 NVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAI--SDKTCAVVLEPIQGEGGVLPAQQA 207
              G PK  +GFGP  EG   V  ND+EAL+ A   +    AV++EPIQGEGG+ P +  
Sbjct: 144 TATGNPKVRNGFGPLLEGFIRVAPNDIEALQEATEGNPNVVAVLMEPIQGEGGLHPMRVE 203

Query: 208 YLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKSLGGGFPIGAML 267
           YL+  RKLCD +  LL+ DEVQ+GMGR G+ FA+   G+VPD+++ AK LG G P+GA+L
Sbjct: 204 YLQQVRKLCDANGWLLMLDEVQAGMGRTGKWFAHQWAGIVPDVMTLAKGLGSGVPVGAVL 263

Query: 268 TTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHERFKSRLQK-IG 326
             G  ++ L  G HG+T+GGNPLA       + ++    +L          K+ LQ+ +G
Sbjct: 264 AHGAASEVLKPGNHGSTFGGNPLAMRAGVETIRIMEEEGLLQNAADVGAHLKAGLQQALG 323

Query: 327 QEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPD-VVRFAPSLVID 385
              G+ +E+RG GL+IG  L      +   VL     +A ++L  + D V+R  P+L + 
Sbjct: 324 SVPGV-NEVRGQGLIIGVEL-----DRPCGVLIDRAAQAGLLLSVTADRVIRLVPALTLT 377

Query: 386 DAEIDE 391
            AE DE
Sbjct: 378 RAEADE 383


Lambda     K      H
   0.318    0.135    0.394 

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: 440
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: 406
Length of database: 398
Length adjustment: 31
Effective length of query: 375
Effective length of database: 367
Effective search space:   137625
Effective search space used:   137625
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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