GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Malonomonas rubra DSM 5091

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV

Query= TCDB::A3ZI83
         (242 letters)



>NCBI__GCF_900142125.1:WP_072908814.1
          Length = 415

 Score =  144 bits (363), Expect = 3e-39
 Identities = 82/222 (36%), Positives = 126/222 (56%), Gaps = 4/222 (1%)

Query: 17  LKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVVNN---LVLNHKNKIEI 73
           +++ +  + +GE  VI+G SGSGKST +R +N L E +SG+V+++    + +N    +++
Sbjct: 46  VQDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKV 105

Query: 74  CRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKYLKVVGLLDKANVYP 133
            R   +MVFQ F L PHMTVLQN     +++    K+  E+ A + L+ VGL   A   P
Sbjct: 106 RRAKLSMVFQSFALMPHMTVLQNAAFG-LEMDGVDKQTREQRALQALEQVGLEAWAESMP 164

Query: 134 ATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMKEISHQSNTTMVVVT 193
             LSGG QQRV +AR L      +L DE  SALDP    E+ D + ++  ++  T+V ++
Sbjct: 165 DELSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFIS 224

Query: 194 HEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLF 235
           H++  A  + DRI  ME G +V+   P E   NP  +  R F
Sbjct: 225 HDLDEAMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAF 266


Lambda     K      H
   0.317    0.133    0.372 

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: 206
Number of extensions: 11
Number of successful extensions: 3
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: 242
Length of database: 415
Length adjustment: 27
Effective length of query: 215
Effective length of database: 388
Effective search space:    83420
Effective search space used:    83420
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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