GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Dyella japonica UNC79MFTsu3.2

Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein

Query= CharProtDB::CH_024626
         (378 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1085
          Length = 336

 Score =  151 bits (381), Expect = 3e-41
 Identities = 88/244 (36%), Positives = 140/244 (57%), Gaps = 10/244 (4%)

Query: 17  LVQLAGIRKCF--DGKEV--IPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSG 72
           +++   + K +  DGK++  +    L I +GE   ++G SG GK+T++RLI  LE    G
Sbjct: 1   MIRFVDVHKSYRVDGKDIPALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGG 60

Query: 73  RIMLDNEDITHVP-----AENRYVNTVFQSYALFPHMTVFENVAFGLRMQ-KTPAAEITP 126
            I++D  ++T +      A+ R +  +FQ + L    TV +N+AF LR+  +T A +I  
Sbjct: 61  SILIDGTEMTALGDAALRAQRRRIGMIFQHFNLLSSQTVADNIAFPLRLAGETDAGKIKA 120

Query: 127 RVMEALRMVQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQM 186
           RV E LR V LE  A + P QLSGGQ+QRV IARA+ N+P +LL DE+ SALD +    +
Sbjct: 121 RVDELLRRVGLEAHASKYPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTASV 180

Query: 187 QNELKALQRKLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAG 246
              L  + R+L +T V +TH+ +    + DR+ V+  GRI + G   +++  P++     
Sbjct: 181 LELLAEINRELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPTTRR 240

Query: 247 FIGE 250
           F+ E
Sbjct: 241 FVNE 244


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: 270
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: 336
Length adjustment: 29
Effective length of query: 349
Effective length of database: 307
Effective search space:   107143
Effective search space used:   107143
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 Sep 17 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