GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltJ in Dinoroseobacter shibae DFL-12

Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate 3606889 Dshi_0319 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= TCDB::Q88NY3
         (248 letters)



>lcl|FitnessBrowser__Dino:3606889 Dshi_0319 polar amino acid ABC
           transporter, inner membrane subunit (RefSeq)
          Length = 411

 Score = 88.6 bits (218), Expect = 2e-22
 Identities = 50/128 (39%), Positives = 74/128 (57%), Gaps = 1/128 (0%)

Query: 111 LISVVICLGLFTAARVCEQVRTGIQALPKGQEAAARAMGFSLPQIYNNVLLPQAYRIIIP 170
           LI++   L L+T A + E VR GI A+ KGQ  AA A+G    +I + ++LPQA R+IIP
Sbjct: 279 LIALWFALALYTGAFIAENVRAGILAVSKGQTEAAAALGMRPNRIMSLIILPQALRVIIP 338

Query: 171 PLTSEFLNVFKNSSVASLIGLMELLAQT-KQTAEFSANLFEAFTLATLIYFTLNMGLMLL 229
           P+ S++LN+ KNSS+A+ IG M+L       T   +   FE   L  L Y  +++ +  L
Sbjct: 339 PVISQYLNLTKNSSLAAAIGYMDLTGTLGGVTLNQTGRSFECVLLLMLFYLLISLSISAL 398

Query: 230 MRMVEKKV 237
           M +    V
Sbjct: 399 MNLYNNAV 406



 Score = 50.8 bits (120), Expect = 4e-11
 Identities = 26/77 (33%), Positives = 45/77 (58%)

Query: 18  SETYLDWYITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPL 77
           ++T++     GL  T+ +A    I A + G L GV+R   N LV+ + + YVE+FRN+P+
Sbjct: 87  TDTHMRAAFVGLLNTLLVAFLGCITATIFGVLAGVLRLSKNWLVAKVMSVYVEIFRNIPV 146

Query: 78  LVQLFIWYFLVPDLLPE 94
           L+ + I   ++   LP+
Sbjct: 147 LIWIVIISAVMSQALPQ 163


Lambda     K      H
   0.325    0.139    0.425 

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: 228
Number of extensions: 10
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: 248
Length of database: 411
Length adjustment: 27
Effective length of query: 221
Effective length of database: 384
Effective search space:    84864
Effective search space used:    84864
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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 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