GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Sinorhizobium meliloti 1021

Align AapM, 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 SMc03865 SMc03865 amino-acid transport system permease ABC transporter protein

Query= TCDB::Q52814
         (384 letters)



>FitnessBrowser__Smeli:SMc03865
          Length = 273

 Score =  112 bits (281), Expect = 9e-30
 Identities = 64/189 (33%), Positives = 112/189 (59%), Gaps = 19/189 (10%)

Query: 167 VETPLWGGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITV 226
           V T +  GL VT+ ++ VG  ++  +G+ +AL   S   V+R +   + EVIRGVP++ +
Sbjct: 42  VFTVVLKGLGVTVFVTLVGFVLATVLGLGVALMALSEHVVLRQIARFYTEVIRGVPILVL 101

Query: 227 LF------------MASVMLPLFLPTGW-------NVDKLLRALIGVSIFTSAYMAEVIR 267
           LF            +A+ +    +  GW       +V  + RA++ + I  SA++AEV R
Sbjct: 102 LFYIAFVGAPALVTVANFVAAPLISAGWIEPFVVRDVSLMWRAIMALMIGYSAFIAEVFR 161

Query: 268 GGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGM 327
            G+Q++ KGQ E A +LGL  +Q+ RL++ PQAI++++P + N F+   KD+SLV+++G+
Sbjct: 162 AGIQSVDKGQVEAAKALGLSRYQRFRLVVFPQAIRVILPPLGNDFVAMVKDSSLVSVLGV 221

Query: 328 FDLLGIVKL 336
            D+  + K+
Sbjct: 222 ADITQMGKV 230


Lambda     K      H
   0.330    0.145    0.469 

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: 255
Number of extensions: 11
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: 384
Length of database: 273
Length adjustment: 28
Effective length of query: 356
Effective length of database: 245
Effective search space:    87220
Effective search space used:    87220
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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