GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Mesorhizobium ciceri WSM1271

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 YP_004134424.1 Mesci_6256 abc transporter related protein

Query= TCDB::Q52815
         (257 letters)



>NCBI__GCF_000185905.1:YP_004134424.1
          Length = 247

 Score =  348 bits (893), Expect = e-101
 Identities = 166/244 (68%), Positives = 197/244 (80%)

Query: 13  ATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKG 72
           + E  +E   ++KWYG FH L+DINL V +GERIVI GPSGSGKST+IRC NRLE HQ+G
Sbjct: 2   SAETIIEARAVSKWYGQFHALKDINLTVHKGERIVICGPSGSGKSTLIRCFNRLESHQEG 61

Query: 73  KIVVDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEV 132
            I V+G  L   +K + +VR  VGMVFQHFNLFPHLT+L NC   P+WV+ +   +A + 
Sbjct: 62  DIAVNGIHLHPKMKNVADVRSNVGMVFQHFNLFPHLTVLMNCMAGPMWVKGVSAAEARKT 121

Query: 133 AMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVL 192
           A+ FL+RV+IPEQANK+P QLSGGQQQRVAIARSLCM P +MLFDEPTSALDPEM+ EVL
Sbjct: 122 ALQFLERVRIPEQANKFPVQLSGGQQQRVAIARSLCMEPAVMLFDEPTSALDPEMVSEVL 181

Query: 193 DTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFL 252
           DTM GLA +GMTM+CVTHEMGFAR VA+RVI MD GQIVE+ +P +FF NPQH+RTKLFL
Sbjct: 182 DTMTGLARDGMTMVCVTHEMGFARAVADRVILMDAGQIVEEGKPDSFFGNPQHDRTKLFL 241

Query: 253 SQIL 256
           SQIL
Sbjct: 242 SQIL 245


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: 235
Number of extensions: 4
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: 247
Length adjustment: 24
Effective length of query: 233
Effective length of database: 223
Effective search space:    51959
Effective search space used:    51959
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