GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Geotalea uraniireducens Rf4

Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein

Query= CharProtDB::CH_024626
         (378 letters)



>NCBI__GCF_000016745.1:WP_011938227.1
          Length = 353

 Score =  221 bits (563), Expect = 2e-62
 Identities = 122/283 (43%), Positives = 178/283 (62%), Gaps = 7/283 (2%)

Query: 32  VIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLDNEDI------THVP 85
           ++  + L +N GE + LLGPSG GKTT+LR IAGLE    G I +  + +        V 
Sbjct: 20  ILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHGSIRIGEQMVFESAKKIEVS 79

Query: 86  AENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLETFAQRKP 145
            E R +  VFQSYAL+PH TV+ENVA+GL+++K P  EI  RV E L  + L   ++R P
Sbjct: 80  VEKRCLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIRQRVQEVLANLGLGDLSERHP 139

Query: 146 HQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLGITFVFVT 205
           HQLSGGQQQRVA+AR++V  P+++LLDE LS LD KLR++ +  L+ L   L ++ V VT
Sbjct: 140 HQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREEARIWLRQLIIDLNLSAVCVT 199

Query: 206 HDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNATVIERLDEQ 265
           HDQ EA+ M+D++V+++DG IEQ GTP+E+Y  PK+LFVA F+G  N  +  V + +D  
Sbjct: 200 HDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVAEFMGANNTISGLVTD-VDGD 258

Query: 266 RVRANVEGRECNIYVNFAVEPGQKLHVLLRPEDLRVEEINDDN 308
             R    G      +   ++ G +   ++R E +++ +   +N
Sbjct: 259 SARIEGNGWALRGRLRTPLKAGDRATAVVRLEKIKLAQTPKEN 301


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: 303
Number of extensions: 13
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: 378
Length of database: 353
Length adjustment: 30
Effective length of query: 348
Effective length of database: 323
Effective search space:   112404
Effective search space used:   112404
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: 49 (23.5 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