GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Desulfovibrio vulgaris Miyazaki F

Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate 8500595 DvMF_1343 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= TCDB::Q88NY3
         (248 letters)



>FitnessBrowser__Miya:8500595
          Length = 337

 Score =  131 bits (330), Expect = 2e-35
 Identities = 73/211 (34%), Positives = 123/211 (58%), Gaps = 4/211 (1%)

Query: 26  ITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPLLVQLFIWY 85
           + GL  T+ +++ A I  +++G + G+ R   N ++   A  Y+E+ R  PLLVQ+F+WY
Sbjct: 128 LEGLWITLEVSVLAIIGGIVIGVVTGLCRISINPMLRWGAITYIEIIRGSPLLVQIFLWY 187

Query: 86  FLVPDLLPEGLQEWFKQDLNPTTSALISVVICLGLFTAARVCEQVRTGIQALPKGQEAAA 145
           F+V  L+   L+      ++P    L   V+ L LFT A V E VR GIQ++ +GQ  AA
Sbjct: 188 FVVGTLINALLEHVGLGGISP----LWYGVMALALFTGAYVAEIVRAGIQSVHRGQMEAA 243

Query: 146 RAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFS 205
           R++G +  Q    V+LPQA+R I+PPL  +F+++ K+SS+  +I + EL   T++    S
Sbjct: 244 RSLGMNYAQAMRKVILPQAFRRIMPPLAGQFISLIKDSSLLGVIAIRELTKATREVVTTS 303

Query: 206 ANLFEAFTLATLIYFTLNMGLMLLMRMVEKK 236
              FE + +  ++Y  L   L L ++ +E++
Sbjct: 304 LQPFELWIVCAVLYLVLTFTLSLFVQYLERR 334


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: 188
Number of extensions: 4
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: 248
Length of database: 337
Length adjustment: 26
Effective length of query: 222
Effective length of database: 311
Effective search space:    69042
Effective search space used:    69042
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