GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Desulfacinum infernum DSM 9756

Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= CharProtDB::CH_024626
         (378 letters)



>NCBI__GCF_900129305.1:WP_073038605.1
          Length = 368

 Score =  241 bits (615), Expect = 2e-68
 Identities = 136/289 (47%), Positives = 182/289 (62%), Gaps = 8/289 (2%)

Query: 18  VQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLD 77
           ++L  + K F    V+    LT+ + EF+ L+GPSGCGK+T LR+IAGLE V SG I + 
Sbjct: 4   IKLDQVNKRFKKNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSGEISIG 63

Query: 78  NEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQL 137
              + HVP ++R +  VFQSYAL+PHM V++N+AFGL  +  P  EI  RV +A  ++ +
Sbjct: 64  GRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAAEILGI 123

Query: 138 ETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKL 197
               QR+P QLSGGQ+QRVA+ RA+V  P+  L DE LS LD KLR QM+ EL  L  +L
Sbjct: 124 SDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAKLHERL 183

Query: 198 GITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNAT 257
             T V+VTHDQ EA+T++DRIVVM+DG+I Q G P E+YE P N FVAGFIG  +M    
Sbjct: 184 QSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPSMNFLD 243

Query: 258 VIERLDEQRVRANVEGRECNIYVNFAVEPGQKLHVL------LRPEDLR 300
           V  RL E+     V+G    + V     P  + HV       +RPED++
Sbjct: 244 V--RLVEEAGDLWVDGESFRLKVPRHRAPAFRGHVNRPVIFGIRPEDVK 290


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: 339
Number of extensions: 13
Number of successful extensions: 1
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: 368
Length adjustment: 30
Effective length of query: 348
Effective length of database: 338
Effective search space:   117624
Effective search space used:   117624
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: 50 (23.9 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