GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapJ in Desulfovibrio vulgaris Hildenborough

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 207829 DVU2342 amino acid ABC transporter, periplasmic amino acid-binding protein

Query= TCDB::Q52812
         (341 letters)



>MicrobesOnline__882:207829
          Length = 270

 Score =  102 bits (254), Expect = 1e-26
 Identities = 73/244 (29%), Positives = 116/244 (47%), Gaps = 14/244 (5%)

Query: 1   MKNKLLSAAIGAAVLAVGASAASATTLSDVKAKGFVQCGVNTGLTGFAAPD-ASGNWAGF 59
           MK  LL A     VL   A+ A A  L ++K +G + CGV   +  F   D  S    GF
Sbjct: 1   MKRLLLLALTLGLVLT--AAVAHAGKLDEIKQRGTLVCGVKDSVVPFGFIDETSKQLVGF 58

Query: 60  DVDFCKAVASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFR 119
           DVD C+ +A        K++     +  R   L  G +D+++   T    RD  + F+  
Sbjct: 59  DVDICQFIADRA---GVKLEVKTVTSATRIPMLTQGSVDLVAATMTHKFERDDVIDFS-- 113

Query: 120 PVTYYD-GQGFMVRKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFEN 178
            +TY+D GQ  +V+KG  +KSA +L G  +    G+T+E N+    K        V F+ 
Sbjct: 114 -ITYFDAGQRLLVKKGGGIKSAADLKGKKVATVKGSTSEKNM----KAAQPDCVVVSFDE 168

Query: 179 LPEVNAAYDAGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWF 238
            P+   A   G+ +  TTD+  L  L+ +   PD+  I+ + I+ EP G  + + D ++ 
Sbjct: 169 YPQAFLALKQGKAEAVTTDEPILVGLKNSDPEPDKWDIVGDFIASEPYGLGLVENDSKFR 228

Query: 239 DIVS 242
           D V+
Sbjct: 229 DFVN 232


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: 195
Number of extensions: 11
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: 270
Length adjustment: 27
Effective length of query: 314
Effective length of database: 243
Effective search space:    76302
Effective search space used:    76302
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: 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