GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Pseudomonas litoralis 2SM5

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_090275879.1 BLU11_RS18455 methionine ABC transporter ATP-binding protein

Query= TCDB::Q9KKE1
         (275 letters)



>NCBI__GCF_900105005.1:WP_090275879.1
          Length = 334

 Score =  167 bits (422), Expect = 4e-46
 Identities = 94/223 (42%), Positives = 138/223 (61%), Gaps = 2/223 (0%)

Query: 43  LNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAF 102
           L+   L I AG+++ I+G SG+GKSTL+R INRL EP++G ++  G++   L A+ LR F
Sbjct: 21  LHATDLTIEAGQVYGIIGHSGAGKSTLLRLINRLEEPSNGRIMVAGEDTTALNAEGLRRF 80

Query: 103 RMRRVSMVFQSFALMPHRTVLQNVVYGQRVRG-VSKDDAREIGMKWIDTVGLSGYDAKFP 161
           R +RV M+FQ F L+   TV  NV    R+ G  ++          +D VGLS + +K+P
Sbjct: 81  R-QRVGMIFQHFNLLSSATVADNVALPLRLAGSANRQQIAARVASLLDRVGLSDHASKYP 139

Query: 162 HQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFIT 221
            QLSGG KQRVG+ARALA +  ++L DEA SALDP   G +   L ++ R L  TIV IT
Sbjct: 140 AQLSGGQKQRVGIARALATEPSILLCDEATSALDPHTTGQVLQLLSEINRELNLTIVLIT 199

Query: 222 HDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264
           H++D   R+  ++A++  G++V+ GT  D+  +P +     FV
Sbjct: 200 HEMDVIRRVCDQVAVMDGGRIVEQGTVADVFLHPQHPTTRSFV 242


Lambda     K      H
   0.323    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: 258
Number of extensions: 14
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: 275
Length of database: 334
Length adjustment: 27
Effective length of query: 248
Effective length of database: 307
Effective search space:    76136
Effective search space used:    76136
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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