GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Malonomonas rubra DSM 5091

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV

Query= TCDB::P31134
         (377 letters)



>NCBI__GCF_900142125.1:WP_072908814.1
          Length = 415

 Score =  181 bits (460), Expect = 2e-50
 Identities = 104/254 (40%), Positives = 149/254 (58%), Gaps = 7/254 (2%)

Query: 8   PQAKTRKALTPL-LEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLA 66
           PQ K   AL    L+   + +  +    V D S  I+KGEIF ++G SG GKST++RML 
Sbjct: 18  PQPKKAMALLKQGLDKEAIFEKTETTVGVQDASFEIFKGEIFVIMGLSGSGKSTMVRMLN 77

Query: 67  GFEQPSAGQIMLDGVDL------SQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDK 120
              +P++GQ+++DG D+        V      ++M+FQS+AL PHMTV QN AFGL+ D 
Sbjct: 78  RLIEPTSGQVLIDGEDIVAMNDDQLVKVRRAKLSMVFQSFALMPHMTVLQNAAFGLEMDG 137

Query: 121 LPKAEIASRVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGAL 180
           + K     R  + L  V ++ +A+  P +LSGG +QRV LAR LA  P +LL+DE   AL
Sbjct: 138 VDKQTREQRALQALEQVGLEAWAESMPDELSGGMQQRVGLARGLAVDPDILLMDEAFSAL 197

Query: 181 DKKLRDRMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEH 240
           D  +R  MQ E++ +  +   T V ++HD +EAM +  RIAIM  G+ VQ+G PEEI ++
Sbjct: 198 DPLIRTEMQDELLKLQAKAKRTIVFISHDLDEAMRIGDRIAIMEGGRVVQVGTPEEILQN 257

Query: 241 PTTRYSAEFIGSVN 254
           P   Y   F   V+
Sbjct: 258 PADDYVRAFFRGVD 271


Lambda     K      H
   0.321    0.137    0.400 

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: 366
Number of extensions: 20
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: 377
Length of database: 415
Length adjustment: 31
Effective length of query: 346
Effective length of database: 384
Effective search space:   132864
Effective search space used:   132864
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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