GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapP in Sinorhizobium meliloti 1021

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 SMa0083 SMa0083 ABC transporter ATP-binding protein

Query= TCDB::Q52815
         (257 letters)



>lcl|FitnessBrowser__Smeli:SMa0083 SMa0083 ABC transporter
           ATP-binding protein
          Length = 259

 Score =  348 bits (894), Expect = e-101
 Identities = 172/243 (70%), Positives = 201/243 (82%)

Query: 13  ATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKG 72
           A + AV +  +NKWY  FH L++I+L V RGERIVI GPSGSGKST+IRCIN+LE    G
Sbjct: 16  ALDPAVRMEGVNKWYDAFHALKNIDLTVGRGERIVICGPSGSGKSTLIRCINQLETIHSG 75

Query: 73  KIVVDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEV 132
           +IVVDG +LT   + +D VR+E GMVFQ FNLFPH+T+LENCTLAP+ VR + K +AEE 
Sbjct: 76  RIVVDGHDLTAGGRNVDLVRQETGMVFQQFNLFPHMTVLENCTLAPMKVRGLAKAEAEET 135

Query: 133 AMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVL 192
           AM +LKRV+IPEQA KYP QLSGGQQQRVAIAR+LCMNPKIMLFDEPTSALDPEM+KEVL
Sbjct: 136 AMKYLKRVRIPEQAVKYPAQLSGGQQQRVAIARALCMNPKIMLFDEPTSALDPEMVKEVL 195

Query: 193 DTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFL 252
           DTMV LA EGMTMLCVTHEMGFAR VA+RV+FMD+G+++E   P AFF  PQHERT+ FL
Sbjct: 196 DTMVDLANEGMTMLCVTHEMGFARSVADRVVFMDRGEVLEIAPPDAFFGAPQHERTRFFL 255

Query: 253 SQI 255
            QI
Sbjct: 256 GQI 258


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: 247
Number of extensions: 9
Number of successful extensions: 1
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: 259
Length adjustment: 24
Effective length of query: 233
Effective length of database: 235
Effective search space:    54755
Effective search space used:    54755
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: 47 (22.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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