GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Paucidesulfovibrio gracilis DSM 16080

Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein

Query= CharProtDB::CH_024626
         (378 letters)



>NCBI__GCF_900167125.1:WP_200806763.1
          Length = 406

 Score =  281 bits (720), Expect = 2e-80
 Identities = 151/328 (46%), Positives = 210/328 (64%), Gaps = 7/328 (2%)

Query: 16  PLVQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIM 75
           P V+L G+ K F     + + DLTI  GE +TLLGPSGCGKTT+LR+IAGLET   G I 
Sbjct: 43  PAVRLQGLMKRFGKTVAVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIY 102

Query: 76  LDNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMV 135
           +    I   P   R +  +FQ+YALFPH T+FENVAFGL+ +     E+  +V +AL MV
Sbjct: 103 IKGRRINDTPIHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMV 162

Query: 136 QLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQR 195
           +L    +R   QLSGGQQQR+A+ARA+V +P +LL+DE LSALD KLR++M+ E+  +Q+
Sbjct: 163 RLPGVEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQ 222

Query: 196 KLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFN 255
           +L +T +FVTHDQ EAL+MS++IVVM+DGR +Q+GTP ++Y+ P N FVA F+G  N F+
Sbjct: 223 QLNLTTLFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADFLGHANFFD 282

Query: 256 ATVIERLDEQRVRANV-EGRECNIYVNFAVEPGQKLHVLLRPEDLRV------EEINDDN 308
           A V+E LD  +VR  + EG E           GQ +H+++R + + V      +E  +  
Sbjct: 283 ARVLEVLDNDQVRVRIAEGLEFTADHVGRWRQGQDVHLVMRAQKINVTSPDLADEELEST 342

Query: 309 HAEGLIGYVRERNYKGMTLESVVELENG 336
                 G + +R+Y G      VEL NG
Sbjct: 343 DLNYYPGKIYDRSYMGGETSYFVELANG 370


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: 391
Number of extensions: 11
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: 406
Length adjustment: 31
Effective length of query: 347
Effective length of database: 375
Effective search space:   130125
Effective search space used:   130125
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