GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badI in Marinobacter adhaerens HP15

Align BadI (characterized)
to candidate GFF4202 HP15_4142 naphthoate synthase

Query= metacyc::MONOMER-892
         (260 letters)



>FitnessBrowser__Marino:GFF4202
          Length = 260

 Score =  370 bits (950), Expect = e-107
 Identities = 174/260 (66%), Positives = 212/260 (81%)

Query: 1   MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60
           M +ED++Y+  NGVA I INRPD+ NAFRG TC EL+ A  +AG++KD+G IV  GAG++
Sbjct: 1   MTYEDILYDENNGVATITINRPDRYNAFRGQTCMELLDAFNRAGWNKDIGVIVFTGAGEK 60

Query: 61  AFCTGGDQSTHDGNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICDL 120
           AFCTGGDQ  H+G YDGRG +GLP+EEL   IR+VPKPVIARV G+AIGGG+VL  ICDL
Sbjct: 61  AFCTGGDQGAHEGQYDGRGLIGLPVEELQRTIREVPKPVIARVNGFAIGGGHVLHVICDL 120

Query: 121 TICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLANL 180
           +I SE AIFGQVGPK+GSVDPG+GTA+LARVVGEK+AREIWY+C++YS ++A   GL N 
Sbjct: 121 SIASETAIFGQVGPKVGSVDPGFGTAYLARVVGEKRAREIWYLCRKYSAQQALEWGLVNA 180

Query: 181 CVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYALKLYYDTDES 240
            VP ++LD EVQKW EE+ E+SPTA++IAKRSFN D+ + AGI  +GM AL LYYDTDES
Sbjct: 181 VVPPEQLDEEVQKWCEEILEKSPTAISIAKRSFNADSDNIAGIGALGMQALSLYYDTDES 240

Query: 241 REGVKALQEKRKPEFRKYIK 260
           +EGV A  EKRKPEFRKY K
Sbjct: 241 KEGVNAFLEKRKPEFRKYYK 260


Lambda     K      H
   0.319    0.138    0.418 

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: 307
Number of extensions: 8
Number of successful extensions: 1
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: 260
Length of database: 260
Length adjustment: 24
Effective length of query: 236
Effective length of database: 236
Effective search space:    55696
Effective search space used:    55696
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 (21.7 bits)
S2: 47 (22.7 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 (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