GapMind for catabolism of small carbon sources

 

Aligments for a candidate for potA in Pseudomonas fluorescens GW456-L13

Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate PfGW456L13_4763 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= CharProtDB::CH_024626
         (378 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4763 Putrescine
           transport ATP-binding protein PotA (TC 3.A.1.11.1)
          Length = 345

 Score =  271 bits (693), Expect = 2e-77
 Identities = 154/358 (43%), Positives = 210/358 (58%), Gaps = 24/358 (6%)

Query: 18  VQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLD 77
           VQ   + + F   + + ++ + I +GEF ++LGPSG GKTT LRLIAG E   +G I + 
Sbjct: 5   VQFTNVSRQFGEVKAVDRVSIDIQDGEFFSMLGPSGSGKTTCLRLIAGFEQPSAGSIRIH 64

Query: 78  NEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQL 137
            E+   +P   R VNTVFQ YALFPHM V +NVA+GL+++    AE   R  EAL MV L
Sbjct: 65  GEEAAGLPPYQRDVNTVFQDYALFPHMNVRDNVAYGLKVKGVGKAERLKRAEEALDMVAL 124

Query: 138 ETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKL 197
             + +RKP QLSGGQ+QRVA+ARA+VN+PR+LLLDE L ALD KLR+QMQ ELK LQR+L
Sbjct: 125 GGYGERKPVQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQGELKKLQRQL 184

Query: 198 GITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNAT 257
           GITF+FVTHDQ EAL+MSDR+ V   GRIEQ  +PR +Y +P   FVA F+G  N+    
Sbjct: 185 GITFIFVTHDQTEALSMSDRVAVFNKGRIEQVDSPRNLYMKPATTFVAEFVGTSNVIRGD 244

Query: 258 VIERLDEQRVRANVEGRECNIYVNFAVEPGQKLHVLLRPEDLRVEEINDDNHAEGLIGYV 317
           +  +L                        G      +RPE +R  E    +H   + G +
Sbjct: 245 LAWQLS-----------------------GNPQPFSIRPEHVRFAEGPLASHEIEVSGLL 281

Query: 318 RERNYKGMTLESVVELENGKMVMVSEFFNE-DDPDFDHSLDQKMAINWVESWEVVLAD 374
            +  Y+G      ++LENG+ + +S+  N+  D    H   Q+++  W     + L D
Sbjct: 282 HDIQYQGSATRYELKLENGQTLNISKANNQWLDTSAQHQTGQRISARWAREAMIPLHD 339


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: 311
Number of extensions: 9
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: 345
Length adjustment: 29
Effective length of query: 349
Effective length of database: 316
Effective search space:   110284
Effective search space used:   110284
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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