GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized)
to candidate H281DRAFT_05872 H281DRAFT_05872 amino acid ABC transporter membrane protein 2, PAAT family

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4772
         (223 letters)



>FitnessBrowser__Burk376:H281DRAFT_05872
          Length = 214

 Score =  118 bits (295), Expect = 1e-31
 Identities = 64/210 (30%), Positives = 110/210 (52%), Gaps = 7/210 (3%)

Query: 11  SLPGLWNGMIMTLKLMAMGVIGGIILGTILALMRLSHNKVLSNIAGAYVNYFRSIPLLLV 70
           SL  L  G++ TL L    ++G  ++G + A++R         IA  Y   FR  P+L+ 
Sbjct: 9   SLSILLQGLVTTLLLSIAAIVGSTLIGLLAAVLRSFGPWGTDRIAKLYTELFRGTPVLIT 68

Query: 71  ITWFYLAVPFVLRWITGEDTPIGAFASCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAQ 130
           + + Y  V +           I  FA+ ++   +++ AY  E+ RAG++S+PKGQ   +Q
Sbjct: 69  LMFIYFGVSYF-------GYAIDVFAAGVIGLSVYQGAYIAEVFRAGIESVPKGQWEVSQ 121

Query: 131 ALGMSYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYAVGLVDFLNASRASGDIIG 190
            LG+S  Q    ++LPQ  R + P L+ Q + L +DTS+V  +G+ + ++  +A  D +G
Sbjct: 122 ILGLSRIQTFASVVLPQTGRIVLPPLVGQYLSLIKDTSIVSMIGMSELMHGGQAIVDRVG 181

Query: 191 RSNEFLIFAGLVYFIISFAASQLVKRLQKR 220
           +  E      L+YF++ F  SQ V+   +R
Sbjct: 182 KPVEIYGLVALIYFVVCFPLSQWVRHHDRR 211


Lambda     K      H
   0.332    0.144    0.428 

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: 134
Number of extensions: 6
Number of successful extensions: 2
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: 223
Length of database: 214
Length adjustment: 22
Effective length of query: 201
Effective length of database: 192
Effective search space:    38592
Effective search space used:    38592
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 45 (21.9 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