GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcC in Nocardioides daejeonensis MJ31

Align carbamate kinase (EC 2.7.2.2) (characterized)
to candidate WP_110208549.1 DNK54_RS18790 carbamate kinase

Query= BRENDA::O96432
         (314 letters)



>NCBI__GCF_003194585.1:WP_110208549.1
          Length = 312

 Score =  242 bits (618), Expect = 7e-69
 Identities = 126/314 (40%), Positives = 191/314 (60%), Gaps = 3/314 (0%)

Query: 1   MRIVVALGGNALLQRGMKGTFQDQQAACRLAMSQIVKIVKDGNELVMTHGNGPQCGAIFL 60
           MR+++ALGGNA+     +   +DQ AA   AM+ +  +++  +++V+THGNGPQ G + +
Sbjct: 1   MRVLMALGGNAMTNAEGRARPEDQIAAAETAMAAVAGLLEHDHDVVVTHGNGPQVGNLLV 60

Query: 61  QNVAGEQEKVPAMPLHVCGAETQGFLGELLQQELDGALRAEGIKKNVVSIVTQSFVDPKD 120
           +N    Q  VP +PL  CGA+TQ  LG +L   LD  L    + +   ++VT++ VD  D
Sbjct: 61  KNELAAQV-VPPVPLDWCGAQTQATLGLILMDALDAELARRHVSRRTATLVTRARVDAAD 119

Query: 121 PAFQNPTKPIGPFYSKEEAEFLRNERGYNMVEDAGRGYRMIVPSPVPQKFVEKEAIKTLV 180
           P F +PTKPIG     EEA+ L  + G    +   +G+R +V SP P + ++  A   L+
Sbjct: 120 PGFTHPTKPIGRHLPAEEAQVLI-DHGETWQDMGAKGWRRVVASPAPLEIIDAPAALALI 178

Query: 181 NSGFIVVCSGGGGIPVILDEQENRIEGVDAVIDKDLGASVLAAATNADAFMILTDVPEAL 240
            +GF+V+ +GGGGIPV+  E +  + GV AVIDKDLGA + A    AD  +I TDVP+A+
Sbjct: 179 EAGFVVIANGGGGIPVVRRE-DGSLTGVPAVIDKDLGAELFARVVGADVLVIATDVPQAV 237

Query: 241 LNYRKENETAIRQATVAEMEKYIEEGHFIKGSMLPKVQACLRFVKSTGKPALITALDCAL 300
           L +       + + T+++M  Y  EGHF  GSM PKV A  RFV++TG+  +IT+L    
Sbjct: 238 LRFGTPEAEPVGEVTLSQMRAYAAEGHFGSGSMGPKVDAVCRFVEATGQVGIITSLSAIT 297

Query: 301 QALKGERGTKIVPN 314
            A+ G+ GT++VP+
Sbjct: 298 DAVHGQAGTRVVPD 311


Lambda     K      H
   0.318    0.136    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: 244
Number of extensions: 15
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: 314
Length of database: 312
Length adjustment: 27
Effective length of query: 287
Effective length of database: 285
Effective search space:    81795
Effective search space used:    81795
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: 48 (23.1 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