GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Paucidesulfovibrio gracilis DSM 16080

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= TCDB::Q9KKE1
         (275 letters)



>NCBI__GCF_900167125.1:WP_078717009.1
          Length = 370

 Score =  171 bits (432), Expect = 3e-47
 Identities = 92/222 (41%), Positives = 136/222 (61%), Gaps = 6/222 (2%)

Query: 43  LNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAF 102
           L+DV L I  G+   I+G SG GK+TL+R +     P+SGE++ DG ++ D+        
Sbjct: 23  LHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEIILDGRSMRDVPPDG---- 78

Query: 103 RMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPH 162
             RRV+ VFQS+AL PH +V  NV +G R+ G+ K +  E   K +  VGL+G   + P 
Sbjct: 79  --RRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMVGLAGQAGRRPT 136

Query: 163 QLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITH 222
            LSGG +QRV +ARA+     V+L+DE  SALD  +R  M+ +L QL+R +  T +F+TH
Sbjct: 137 SLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRREMGITFIFVTH 196

Query: 223 DLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264
           D +EA  +   + ++ +G V QVGTP ++ + P N +VARFV
Sbjct: 197 DQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFV 238


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: 283
Number of extensions: 15
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: 370
Length adjustment: 27
Effective length of query: 248
Effective length of database: 343
Effective search space:    85064
Effective search space used:    85064
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 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