GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Dinoroseobacter shibae DFL-12

Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate 3608832 Dshi_2224 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= reanno::pseudo6_N2E2:Pf6N2E2_2959
         (242 letters)



>FitnessBrowser__Dino:3608832
          Length = 268

 Score = 87.8 bits (216), Expect = 2e-22
 Identities = 72/231 (31%), Positives = 104/231 (45%), Gaps = 18/231 (7%)

Query: 12  SAFSLQGFGPLLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSSVKLLRIPAQLYTTLIR 71
           S F+L     L+  G    +   A +LL    L    A  K S   +LR+PA  +  + R
Sbjct: 25  SDFTLCEQFTLIGSGLIWNVYFGAFALLFGFFLATAVALGKASDRAVLRVPADWFIFVFR 84

Query: 72  GVPDLVLMLLIFYSLQTWLTSLTDFMEWEYIEIDPFG---AGVITLGFIY-GAYFTETFR 127
           G P L +   + Y L   L +++          DPF    AG + + F+   AY  E F 
Sbjct: 85  GSP-LFIQFFLAYFLFIQLKAVSP-------AFDPFTSAWAGALVVLFLNTSAYAGEIFY 136

Query: 128 GAILSVPRGQVEAATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGL 187
           GA+ SVP+G +EAA AYGL    +FR V +P M+R A P   N  + +  AT LV   G 
Sbjct: 137 GALRSVPKGDLEAADAYGLAGWTKFRRVTWPTMLRLAWPSYTNEAIFLFHATTLVFFAGF 196

Query: 188 ------ADLVKAAQDAGKSTYQLFYFLVLAALIYLLITSASNFILRWLERR 232
                  D +  AQ     T+  F    + A  ++L+T A  F+   + RR
Sbjct: 197 PAFQQRGDALYYAQYFADKTFNPFIPYPIVAFYFILLTLAVIFVFSLINRR 247


Lambda     K      H
   0.329    0.142    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: 184
Number of extensions: 11
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: 242
Length of database: 268
Length adjustment: 24
Effective length of query: 218
Effective length of database: 244
Effective search space:    53192
Effective search space used:    53192
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 (21.8 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