GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtB' in Herbaspirillum seropedicae SmR1

Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate HSERO_RS17565 HSERO_RS17565 glutamate/aspartate ABC transporter permease GltJ

Query= uniprot:Q31RP0
         (377 letters)



>FitnessBrowser__HerbieS:HSERO_RS17565
          Length = 241

 Score = 87.4 bits (215), Expect = 4e-22
 Identities = 44/130 (33%), Positives = 78/130 (60%)

Query: 241 LSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALR 300
           ++ +F   +L L  +T A + E +R GI S+P GQ  A  ALGLT  QT   +++P A+R
Sbjct: 103 MTQQFVMAMLCLGMFTAARVCEQVRSGIESLPRGQKGAGLALGLTLGQTYLFVLLPMAMR 162

Query: 301 VIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVI 360
           +++P L S+++   KNS++A  +G  +L A  +  ++ T +P E F+ + L Y+ IN  +
Sbjct: 163 IVLPPLTSEFLNIFKNSAVASTIGLLELAAQGRQLVDYTAQPYEAFIAVTLAYMLINICV 222

Query: 361 SAGMNGLQQR 370
            + M  L+++
Sbjct: 223 MSLMRILERK 232



 Score = 45.4 bits (106), Expect = 2e-09
 Identities = 26/77 (33%), Positives = 39/77 (50%)

Query: 74  TADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTP 133
           T  +Y   L+ GL  ++ +     IL  V+GT  G+     N  L   +  YV + RN P
Sbjct: 16  TGQTYLDWLLSGLGVTVALGLSAWILALVLGTFLGILRTLPNRALSGFAACYVELFRNVP 75

Query: 134 LLLQLIVWYFPILLSLP 150
           LL+Q+ +WYF +   LP
Sbjct: 76  LLVQIFIWYFAMPELLP 92


Lambda     K      H
   0.326    0.140    0.445 

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: 219
Number of extensions: 6
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 377
Length of database: 241
Length adjustment: 27
Effective length of query: 350
Effective length of database: 214
Effective search space:    74900
Effective search space used:    74900
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: 48 (23.1 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