GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Magnetospirillum magneticum AMB-1

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_011383520.1 AMB_RS05625 phosphate ABC transporter ATP-binding protein

Query= TCDB::Q52815
         (257 letters)



>NCBI__GCF_000009985.1:WP_011383520.1
          Length = 260

 Score =  135 bits (341), Expect = 6e-37
 Identities = 81/245 (33%), Positives = 136/245 (55%), Gaps = 18/245 (7%)

Query: 22  NMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEE-----HQKGKIVV 76
           ++N  YG+   L D+NL +  G+   + GPSG GKST +RCINR+ +        G + +
Sbjct: 17  DLNVHYGEKQALFDVNLDIPVGQVTALIGPSGCGKSTFLRCINRMNDLVEIARVSGSLFL 76

Query: 77  DGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAP-IWVRKMPKKQAEEVAMH 135
           DG ++ +    + ++R  VGMVFQ  N FP  +I EN    P +        + +E+ + 
Sbjct: 77  DGIDIQDAAMDVVQLRARVGMVFQRPNPFPK-SIYENVAFGPRLHGLAAGADELDEIVIS 135

Query: 136 FLKRV----KIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDP---EMI 188
            L +     ++ ++  +    LSGGQQQR+ IAR++ + P+++L DEP SALDP     +
Sbjct: 136 SLDKAGLWGEVKDRMGETGTSLSGGQQQRLCIARAIAVAPEVILMDEPCSALDPIATAAV 195

Query: 189 KEVLDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERT 248
           +E++D + G      T++ VTH M  A +V+ R  F   G+++E  E  + F +PQH  T
Sbjct: 196 EELIDELRG----SYTIVIVTHSMQQAARVSQRTGFFHLGKLIEMGETESMFTSPQHPLT 251

Query: 249 KLFLS 253
           + +++
Sbjct: 252 QGYIT 256


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: 160
Number of extensions: 5
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: 260
Length adjustment: 24
Effective length of query: 233
Effective length of database: 236
Effective search space:    54988
Effective search space used:    54988
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