GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Hydrogenovibrio kuenenii DSM 12350

Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate WP_024851725.1 N745_RS0108650 ABC transporter ATP-binding protein

Query= CharProtDB::CH_024626
         (378 letters)



>NCBI__GCF_000526715.1:WP_024851725.1
          Length = 282

 Score =  151 bits (382), Expect = 2e-41
 Identities = 90/221 (40%), Positives = 136/221 (61%), Gaps = 16/221 (7%)

Query: 20  LAGIRKCFDGK----EVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIM 75
           ++G+ K F  K    EV+  +DLT+   EF+ L+G SGCGK+T+LR+I GLE +  G+++
Sbjct: 7   ISGLNKTFITKKGAVEVLESIDLTVKENEFVALVGASGCGKSTLLRIIGGLEKLTKGQVL 66

Query: 76  LDNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKT-------PAAEITPRV 128
           +D E+I + P ++R +  VFQ Y+L+P +TV EN+ F   ++             +  R 
Sbjct: 67  VD-EEIVNKPGKDRAM--VFQDYSLYPWLTVKENIQFSRNLKINGQGNGLGDIGSMVDRS 123

Query: 129 MEALRMVQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQN 188
              L ++ LE      P+QLSGG +QRVAIARA+++KP +LL+DE   ALD + R+ M +
Sbjct: 124 YALLDLMGLEKVQDSHPNQLSGGMRQRVAIARALMSKPDVLLMDEPFGALDAQTREVMHD 183

Query: 189 ELKALQRKLGITFVFVTHDQEEALTMSDRIVVM--RDGRIE 227
            +  L      T VFVTHD EEA+ ++DR+VVM    GRI+
Sbjct: 184 LILHLFEIEKSTIVFVTHDVEEAIYLADRVVVMAPNPGRID 224


Lambda     K      H
   0.319    0.136    0.385 

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: 232
Number of extensions: 13
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: 378
Length of database: 282
Length adjustment: 28
Effective length of query: 350
Effective length of database: 254
Effective search space:    88900
Effective search space used:    88900
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 (21.7 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