GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapP in Pseudomonas stutzeri RCH2

Align AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate GFF3101 Psest_3160 ABC-type polar amino acid transport system, ATPase component

Query= TCDB::Q52815
         (257 letters)



>lcl|FitnessBrowser__psRCH2:GFF3101 Psest_3160 ABC-type polar amino
           acid transport system, ATPase component
          Length = 255

 Score =  399 bits (1024), Expect = e-116
 Identities = 186/245 (75%), Positives = 223/245 (91%)

Query: 13  ATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKG 72
           A+   +++  ++KW+G FHVL+DINL V +GERIV+ GPSGSGKST IRC+NRLEEHQ+G
Sbjct: 11  ASGPVIQMQGVHKWFGQFHVLKDINLSVRQGERIVLCGPSGSGKSTTIRCLNRLEEHQQG 70

Query: 73  KIVVDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEV 132
           +IV++G ELT+DLK+I+ +R EVGMVFQHFNLFPHLT+L+NCTLAP+WVRK+P++QAEE+
Sbjct: 71  RIVINGVELTSDLKQIEAIRSEVGMVFQHFNLFPHLTVLQNCTLAPMWVRKLPRRQAEEI 130

Query: 133 AMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVL 192
           AMH+L+RV+IPEQANK+PGQLSGGQQQRVAIAR+LCM PKIMLFDEPTSALDPEM+KEVL
Sbjct: 131 AMHYLERVRIPEQANKFPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVL 190

Query: 193 DTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFL 252
           DTMV LAE GMTMLCVTHEMGFAR VA+RVIFMD+G+IVEQ EP  FF NP ++RTKLFL
Sbjct: 191 DTMVSLAESGMTMLCVTHEMGFARTVADRVIFMDKGEIVEQAEPEMFFTNPVNDRTKLFL 250

Query: 253 SQILH 257
           SQILH
Sbjct: 251 SQILH 255


Lambda     K      H
   0.321    0.135    0.394 

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: 277
Number of extensions: 5
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: 257
Length of database: 255
Length adjustment: 24
Effective length of query: 233
Effective length of database: 231
Effective search space:    53823
Effective search space used:    53823
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 (21.9 bits)
S2: 47 (22.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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