GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltI in Desulfovibrio vulgaris Hildenborough

Align glutamate-aspartate periplasmic-binding protein (characterized)
to candidate 207829 DVU2342 amino acid ABC transporter, periplasmic amino acid-binding protein

Query= CharProtDB::CH_002441
         (302 letters)



>lcl|MicrobesOnline__882:207829 DVU2342 amino acid ABC transporter,
           periplasmic amino acid-binding protein
          Length = 270

 Score =  146 bits (368), Expect = 6e-40
 Identities = 93/262 (35%), Positives = 141/262 (53%), Gaps = 14/262 (5%)

Query: 10  ILALALSAGLAQADDAAPAAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQK-VVGYSQD 68
           +L LAL+ GL     AA A    LD+I + G +V G ++S VPF + D   K +VG+  D
Sbjct: 4   LLLLALTLGLVLT--AAVAHAGKLDEIKQRGTLVCGVKDSVVPFGFIDETSKQLVGFDVD 61

Query: 69  YSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAFSD 128
               I +    KL     +VK +  TS  RIP+L  G+ D    + T+  ER     FS 
Sbjct: 62  ICQFIADRAGVKL-----EVKTV--TSATRIPMLTQGSVDLVAATMTHKFERDDVIDFSI 114

Query: 129 TIFVVGTRLLTKKGGDIKDFANLKDKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHG 188
           T F  G RLL KKGG IK  A+LK K V    G+TSE    K  +  + +  ++S  ++ 
Sbjct: 115 TYFDAGQRLLVKKGGGIKSAADLKGKKVATVKGSTSE----KNMKAAQPDCVVVSFDEYP 170

Query: 189 DSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRKDDPQFKKL 248
            +F  L+ G+A A   D+ +L G +    +PD W+IVG   + E YG  L ++D +F+  
Sbjct: 171 QAFLALKQGKAEAVTTDEPILVGLKNSDPEPDKWDIVGDFIASEPYGLGLVENDSKFRDF 230

Query: 249 MDDTIAQVQTSGEAEKWFDKWF 270
           ++ ++A++ T+G  +K +DKWF
Sbjct: 231 VNKSLAEMWTTGAYQKSYDKWF 252


Lambda     K      H
   0.314    0.130    0.366 

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: 189
Number of extensions: 11
Number of successful extensions: 3
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: 302
Length of database: 270
Length adjustment: 26
Effective length of query: 276
Effective length of database: 244
Effective search space:    67344
Effective search space used:    67344
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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