GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatJ 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)



>MicrobesOnline__882:207829
          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:

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