GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Herbaspirillum seropedicae SmR1

Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate HSERO_RS19245 HSERO_RS19245 glutamate/aspartate transporter permease GltK

Query= TCDB::Q88NY3
         (248 letters)



>FitnessBrowser__HerbieS:HSERO_RS19245
          Length = 231

 Score =  129 bits (324), Expect = 5e-35
 Identities = 74/217 (34%), Positives = 127/217 (58%), Gaps = 7/217 (3%)

Query: 25  YITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPLLVQLFIW 84
           + TGL +T+ +  +A    ++LG+LL +MR   N+ +S IAT YV L R++PL++ +F +
Sbjct: 18  FTTGLKFTLILTFSAMAGGIILGTLLAMMRLSSNKPLSFIATTYVNLIRSIPLVLVIFWF 77

Query: 85  YFLVPDLLPEGLQEWFKQDLNPT-TSALISVVICLGLFTAARVCEQVRTGIQALPKGQEA 143
           YFLVP +       W      P    A  S +I   LF AA  CE +R+GIQ++P+GQ  
Sbjct: 78  YFLVPFI-----GAWMIGASEPIQVGAFQSALITFILFEAAYYCEIMRSGIQSIPRGQVF 132

Query: 144 AARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIG-LMELLAQTKQTA 202
           A  A+G +  Q+  NV+LPQA+R + P L ++ + +F++ S+  ++G + + +    + A
Sbjct: 133 AGYAIGMNYWQMMGNVVLPQAFRNMTPILLTQTIVLFQDVSLVYVLGSVPDFVTSASKIA 192

Query: 203 EFSANLFEAFTLATLIYFTLNMGLMLLMRMVEKKVAV 239
           +    L E +    ++YF L+ GL  L++  +KK+A+
Sbjct: 193 QRDGRLVEMYLFVAVVYFVLSFGLSTLVKRFQKKIAI 229


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: 151
Number of extensions: 8
Number of successful extensions: 3
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: 231
Length adjustment: 23
Effective length of query: 225
Effective length of database: 208
Effective search space:    46800
Effective search space used:    46800
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: 46 (22.3 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