GapMind for catabolism of small carbon sources

 

Alignments 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 SMa0489 SMa0489 ABC transporter ATP-binding protein

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__Smeli:SMa0489
          Length = 255

 Score =  345 bits (884), Expect = e-100
 Identities = 164/242 (67%), Positives = 204/242 (84%)

Query: 15  EVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKI 74
           +  ++++ + K +G F  L+ ++L+V RGE+IV+ GPSGSGKST+IRCINR+EEH  G+I
Sbjct: 12  DTMIQLIGVGKRFGQFEALKQVSLEVRRGEKIVLCGPSGSGKSTLIRCINRMEEHTSGRI 71

Query: 75  VVDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAM 134
           ++DG ELT+  K I+ VRREVGMVFQ FNLFPH+TIL+N T+A   VRK P+K+A+EVAM
Sbjct: 72  IIDGRELTDRTKDINAVRREVGMVFQSFNLFPHMTILKNLTIAQRLVRKTPEKEAKEVAM 131

Query: 135 HFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDT 194
           H+LKRVKIPEQA+KYP QLSGGQQQRVAIAR+LCM P+IMLFDEPTSALDPEMI EVLD 
Sbjct: 132 HYLKRVKIPEQASKYPVQLSGGQQQRVAIARALCMKPQIMLFDEPTSALDPEMISEVLDV 191

Query: 195 MVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQ 254
           MV LA +GMTM+CVTHEMGFAR VA+RV+FMD GQ++E+ +P  FF NP++ERT LFL Q
Sbjct: 192 MVDLARDGMTMICVTHEMGFARSVADRVMFMDGGQLIEEGDPETFFANPRNERTALFLRQ 251

Query: 255 IL 256
           IL
Sbjct: 252 IL 253


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: 244
Number of extensions: 6
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: 255
Length adjustment: 24
Effective length of query: 233
Effective length of database: 231
Effective search space:    53823
Effective search space used:    53823
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 (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