GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Pseudomonas fluorescens FW300-N2E3

Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate AO353_04275 AO353_04275 polyamine ABC transporter ATP-binding protein

Query= CharProtDB::CH_024626
         (378 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04275
          Length = 345

 Score =  273 bits (699), Expect = 4e-78
 Identities = 155/358 (43%), Positives = 208/358 (58%), Gaps = 24/358 (6%)

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

Query: 78  NEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQL 137
             +   +P   R VNTVFQ YALFPHM V +NVA+GL+++    AE   R  EAL MV L
Sbjct: 65  GAEAAGLPPYQRDVNTVFQDYALFPHMNVRDNVAYGLKVKGVGKAERLKRAEEALDMVAL 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  TPR +Y +P   FVA F+G  N+    
Sbjct: 185 GITFIFVTHDQTEALSMSDRVAVFNKGRIEQVDTPRNLYMKPNTTFVAEFVGTSNVIRGE 244

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

Query: 318 RERNYKGMTLESVVELENGKMVMVSEFFNE-DDPDFDHSLDQKMAINWVESWEVVLAD 374
            +  Y+G      ++LENG+ + +S   N+  D    H   Q+++  W     V L D
Sbjct: 282 HDIQYQGSATRYEMKLENGQTLSISHANNQWLDVSVQHQTGQRISARWAREAMVPLHD 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: 308
Number of extensions: 7
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:

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