GapMind for catabolism of small carbon sources

 

Alignments for a candidate for snatA in Methanococcus aeolicus Nankai-3

Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate WP_011973908.1 MAEO_RS06085 NAAT family transporter

Query= TCDB::Q8J305
         (216 letters)



>NCBI__GCF_000017185.1:WP_011973908.1
          Length = 217

 Score =  150 bits (380), Expect = 1e-41
 Identities = 79/206 (38%), Positives = 131/206 (63%), Gaps = 4/206 (1%)

Query: 7   FLKYLILLYGGLFAITNPVGAVPVFLSVTHDLSWRERREIASKTAISVVATLVVFALLGQ 66
           F  + I  +  +F I NP+G VP+F   T +    E+ E+  K+AI+V+ TL+ FAL G 
Sbjct: 7   FFSFFIYSFTSIFIIMNPIGLVPLFYIWTSESEKTEKIELLRKSAIAVMLTLLTFALFGG 66

Query: 67  WIFKFFGSSTDAFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVTLEEVAIIP 126
            IFKFFG + D+F +AGGIL+ ++A DML  ++S  + + ++     EE ++LE++A++P
Sbjct: 67  SIFKFFGITLDSFKVAGGILMLKIAWDMLHAQVSKTRHNLKD----DEEPISLEDIAVVP 122

Query: 127 LAIPLISGPGAITTVMLYMAKSTTNLQRLAVILTIILIGITVWFVLCSANRIKARLGRVG 186
           +AIPL++GPG ITT ++ M  S T    L ++ +IIL  +    +L  ++ I   L   G
Sbjct: 123 MAIPLLAGPGTITTSIILMEHSITTYDTLIIMFSIILATLISVVILYLSDNIARILRVSG 182

Query: 187 IKVMTRMMGLILTSMAVQMIINGIKG 212
           IK + R+MGLIL ++++++I +G+ G
Sbjct: 183 IKAIVRIMGLILAAISIEIISSGVFG 208


Lambda     K      H
   0.327    0.141    0.396 

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: 112
Number of extensions: 6
Number of successful extensions: 2
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: 216
Length of database: 217
Length adjustment: 22
Effective length of query: 194
Effective length of database: 195
Effective search space:    37830
Effective search space used:    37830
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)

This GapMind analysis is from Apr 09 2024. 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