GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Flavobacterium ummariense DS-12

Align AapP, 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_091519040.1 BM253_RS03250 ATP-binding cassette domain-containing protein

Query= TCDB::Q52815
         (257 letters)



>NCBI__GCF_900115115.1:WP_091519040.1
          Length = 227

 Score =  117 bits (292), Expect = 3e-31
 Identities = 69/205 (33%), Positives = 115/205 (56%), Gaps = 7/205 (3%)

Query: 32  VLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGK-IVVDGTELTNDLKKIDE 90
           +L D+N+ + +GE I + G +GSGKS++++ +    + + G+ ++VD    T     I  
Sbjct: 20  ILADVNIDIHKGEFIYLIGKTGSGKSSLMKTLYADLDLKDGEGVIVDYDLRTLKQNDIPF 79

Query: 91  VRREVGMVFQHFNLFPHLTILENCTL---APIWVRKMPKKQAEEVAMHFLKRVKIPEQAN 147
           +RR++G+VFQ F L P   I EN      A  W  ++      E     L RV + +   
Sbjct: 80  LRRKLGIVFQDFKLLPDRNIFENLLFVLKATGWTNEVDMNARIE---DVLDRVGMLQHIR 136

Query: 148 KYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTMVGLAEEGMTMLC 207
           K P Q+SGG+QQRVAIAR+L  +P+++L DEPT  LDP+   EV++ +  + + G T+L 
Sbjct: 137 KMPHQISGGEQQRVAIARALLNDPELILADEPTGNLDPQTSVEVMEVLQQINQNGRTILM 196

Query: 208 VTHEMGFARQVANRVIFMDQGQIVE 232
            TH+     +   + +  D+G++ E
Sbjct: 197 ATHDYALLLKYPAKTLKCDEGKVFE 221


Lambda     K      H
   0.321    0.135    0.394 

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: 143
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: 257
Length of database: 227
Length adjustment: 23
Effective length of query: 234
Effective length of database: 204
Effective search space:    47736
Effective search space used:    47736
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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