GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Rhizorhabdus wittichii RW1

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein

Query= TCDB::P73721
         (252 letters)



>NCBI__GCF_000016765.1:WP_012048833.1
          Length = 241

 Score =  224 bits (571), Expect = 1e-63
 Identities = 120/234 (51%), Positives = 159/234 (67%), Gaps = 3/234 (1%)

Query: 16  KNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVAGVDLSGA 75
           K +G    LR V+ ++   + I I GPSG GKST +RC+N LE    G + +   ++   
Sbjct: 9   KWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIGEDEV--- 65

Query: 76  KIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDRALTYLDKVG 135
           + D++ L+++R RVGMVFQ FNLFPHLT+L+N  LAP KV  +    A+  A   L++V 
Sbjct: 66  RPDRRVLQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVR 125

Query: 136 LGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVLNVMKQLAEE 195
           +  +AD YP QLSGGQ+QR AIAR L M+PEI+LFDEPTSALD E+V EVL++MK LA E
Sbjct: 126 IADQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIMKALATE 185

Query: 196 GMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFLSRI 249
           G+TM  VTHEM FAREV++R+ F + G I E G P + F  P  +R RAFLSR+
Sbjct: 186 GITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRAFLSRL 239


Lambda     K      H
   0.321    0.139    0.397 

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: 186
Number of extensions: 5
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: 252
Length of database: 241
Length adjustment: 24
Effective length of query: 228
Effective length of database: 217
Effective search space:    49476
Effective search space used:    49476
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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