GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruF in Chromobacterium vaccinii MWU205

Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate WP_046157872.1 VL52_RS15515 arginine N-succinyltransferase

Query= CharProtDB::CH_107315
         (338 letters)



>NCBI__GCF_000971335.1:WP_046157872.1
          Length = 348

 Score =  240 bits (612), Expect = 4e-68
 Identities = 135/343 (39%), Positives = 200/343 (58%), Gaps = 7/343 (2%)

Query: 1   MLVMRPAQAADLP---QVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEE 57
           M+ +RP +  DLP   ++ R AA   VG+TSLP + +RL+ +I  S  SF+ E+    + 
Sbjct: 1   MMFIRPVEHKDLPGLMELARSAASGGVGLTSLPINEDRLQKRIARSVLSFSGELD-RADH 59

Query: 58  SYFFVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDL 117
            Y FVLEDS +G++ G  A+ A+ G  EP+Y++R  T VHAS  L ++++   L L +D 
Sbjct: 60  GYVFVLEDSENGKVAGICAVEAAVGLKEPWYNYRIGTIVHASEELGVYSRHETLFLSNDH 119

Query: 118 TGNSLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFW 177
           TG S L + Y+  D        L S+ R LF+A  P+ F   VV E+ G SDE G SPFW
Sbjct: 120 TGYSELCTLYLHPDYRVKRNGGLLSKSRFLFLAQFPQLFGKMVVAEMRGVSDENGRSPFW 179

Query: 178 NAVGRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITF 237
            A+GR+FF +++ EA+ L+G+  + F+AELMP +P+YV  L   AQ  +G  H   +   
Sbjct: 180 EALGRHFFSIDFAEADYLTGIGQKAFVAELMPKHPVYVDFLEPEAQAVIGLTHEATRPAV 239

Query: 238 DILMREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSG--RPYLVTNG 295
            +L  EGF  + Y+DIFD GPT+ A T  IR++ +S+ +P ++ +    G    YLV N 
Sbjct: 240 AMLESEGFRYEGYVDIFDAGPTVQAYTGDIRAVKESQRLPARVVDPLPDGDKECYLVCND 299

Query: 296 QLQDFRAVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLVAV 338
            LQD+RAV+ +    P     L+ E A AL + +G  VR V +
Sbjct: 300 ALQDYRAVLAE-SVRPQGEFCLTPELARALKIKDGDHVRCVTL 341


Lambda     K      H
   0.319    0.135    0.387 

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: 265
Number of extensions: 9
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: 338
Length of database: 348
Length adjustment: 29
Effective length of query: 309
Effective length of database: 319
Effective search space:    98571
Effective search space used:    98571
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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:

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