GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Croceitalea dokdonensis DOKDO 023

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_054557498.1 I595_RS00860 ABC transporter ATP-binding protein

Query= TCDB::Q52815
         (257 letters)



>NCBI__GCF_001306415.1:WP_054557498.1
          Length = 219

 Score =  132 bits (331), Expect = 8e-36
 Identities = 80/220 (36%), Positives = 128/220 (58%), Gaps = 10/220 (4%)

Query: 18  VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGK---I 74
           +   N+ K YGD  VL+ +++ + +GE I I GPSG+GK+T+++ +  L+     K   I
Sbjct: 2   ITATNIKKNYGDLKVLKGVSISIKKGEVISIVGPSGAGKTTLLQLVGTLDTPSNPKDSSI 61

Query: 75  VVDGTELTNDL--KKIDEVRRE-VGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEE 131
           +++G ++T DL  K++ + R E +G +FQ   L P  T LEN  + P +++K PK +AE 
Sbjct: 62  MINGVDVT-DLRDKQLAKFRNENIGFIFQFHQLLPEFTALENVCI-PAFIKKTPKAKAEV 119

Query: 132 VAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEV 191
                L  + + ++ +  P +LSGG+QQRVA+AR+L  NP ++  DEP+  LD E  + +
Sbjct: 120 RGRELLDFLGLSQRYDHRPRELSGGEQQRVAVARALINNPSVIFADEPSGNLDSESAENL 179

Query: 192 LDTMVGLAEE-GMTMLCVTHEMGFARQVANRVIFMDQGQI 230
                 L EE G T + VTH    A  +A+R + M  GQI
Sbjct: 180 HQLFFKLREEFGQTFVIVTHNKELA-NMADRKLIMVDGQI 218


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: 135
Number of extensions: 6
Number of successful extensions: 4
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: 219
Length adjustment: 23
Effective length of query: 234
Effective length of database: 196
Effective search space:    45864
Effective search space used:    45864
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