GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5405 in Rhizobium johnstonii 3841

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate WP_011654832.1 RL_RS30155 amino acid ABC transporter ATP-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_5405
         (254 letters)



>NCBI__GCF_000009265.1:WP_011654832.1
          Length = 254

 Score =  339 bits (870), Expect = 3e-98
 Identities = 169/242 (69%), Positives = 198/242 (81%)

Query: 12  EGIIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRI 71
           E +I M+ V KWYG F  L+DIN++V+ GERIVLCGPSGSGKST IRC+N LE +++G I
Sbjct: 11  ETMITMERVEKWYGAFQALRDINISVRSGERIVLCGPSGSGKSTLIRCINHLETYERGEI 70

Query: 72  VVDGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAM 131
            V G+ L N  K I+AIRREVGMVFQ FNLFPHLT+LQNC LAPM    + + +AEE A 
Sbjct: 71  RVGGILLGNQAKTIDAIRREVGMVFQQFNLFPHLTVLQNCMLAPMKAVGVSRAEAEERAR 130

Query: 132 HYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDT 191
             LERV+I EQA KYP QLSGGQQQRVAIARALCM+PK+MLFDEPTSALDPEMVKEVLDT
Sbjct: 131 GLLERVKILEQADKYPVQLSGGQQQRVAIARALCMRPKVMLFDEPTSALDPEMVKEVLDT 190

Query: 192 MIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFLSQ 251
           MI LA++GMTM+CVTHEMGFAR VA+RVIFM  G IVE+A P +FF NPQ++RT+ FL +
Sbjct: 191 MIALADEGMTMICVTHEMGFARQVADRVIFMASGAIVEEAPPAEFFTNPQHERTRKFLGE 250

Query: 252 IL 253
           IL
Sbjct: 251 IL 252


Lambda     K      H
   0.322    0.137    0.407 

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: 241
Number of extensions: 8
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: 254
Length of database: 254
Length adjustment: 24
Effective length of query: 230
Effective length of database: 230
Effective search space:    52900
Effective search space used:    52900
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 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