GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ 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)



>FitnessBrowser__Dino:3606889
          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:

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