GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapJ in Methylocystis bryophila S285

Align AapJ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate WP_245299991.1 B1812_RS19680 amino acid ABC transporter substrate-binding protein

Query= TCDB::Q52812
         (341 letters)



>NCBI__GCF_002117405.1:WP_245299991.1
          Length = 350

 Score =  301 bits (772), Expect = 1e-86
 Identities = 145/336 (43%), Positives = 209/336 (62%), Gaps = 8/336 (2%)

Query: 11  GAAVLAVGASAASATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGFDVDFCKAVASA 70
           GA  LA    + +++TL +++ +G V CG      GFA  D +G+W+GFD+DFC+A+A A
Sbjct: 18  GAPRLAAQPESKASSTLQEIRRRGVVVCGATAPAPGFAVMDEAGSWSGFDIDFCRALAVA 77

Query: 71  VFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFRPVTYYDGQGFM 130
              DP K++      K+R  AL SG++DVL     WT  R+      +  +++Y GQGF+
Sbjct: 78  ALDDPQKIRIETLQQKQRLPALHSGDVDVLLSGAPWTEAREAGHQLLYGAISFYGGQGFL 137

Query: 131 VRKGLNVKSALELSGAA-----ICVQSGTTTELNLADYFKTNNLQYNPVVFENLPEVNAA 185
            R+     +     GA      +CVQ G ++ELNLA +++ + + Y PV F +L E   A
Sbjct: 138 GRRAWG-PTGEPWRGAGGTPPRVCVQQGGSSELNLAQFYREHGVAYRPVAFGSLEEAARA 196

Query: 186 YDAGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFDIVSWTA 245
           YDAG CD+++ D   L+  R  L+ PD+H++ P +ISK PLGP VRQGDDQWF++V WT 
Sbjct: 197 YDAGDCDLFSADLVELHQWRSRLQKPDDHVVAPALISKSPLGPIVRQGDDQWFNVVRWTL 256

Query: 246 YALINAEEFGITQANVDEMKNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANVIKGVGNY 305
           +A+++AEE G+    VD   +S  PD++R +GS+ D   G  LGL  DWA  VI  VGNY
Sbjct: 257 FAMVDAEELGVDAKTVDAALSSDIPDLRRLVGSDGD--FGEGLGLRPDWAYRVIHEVGNY 314

Query: 306 GEIFERNIGQGSPLKIARGLNALWNKGGIQYAPPVR 341
            E+F+RN+G+ SP  + R  NALW+KGG+ YAPPVR
Sbjct: 315 AEVFDRNLGKSSPFAMERRQNALWSKGGLMYAPPVR 350


Lambda     K      H
   0.316    0.134    0.398 

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: 311
Number of extensions: 9
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: 341
Length of database: 350
Length adjustment: 29
Effective length of query: 312
Effective length of database: 321
Effective search space:   100152
Effective search space used:   100152
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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