GapMind for catabolism of small carbon sources

 

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

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate PfGW456L13_3911 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= uniprot:A0A166R419
         (517 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3911 Ribose ABC
           transport system, ATP-binding protein RbsA (TC
           3.A.1.2.1)
          Length = 517

 Score =  920 bits (2378), Expect = 0.0
 Identities = 475/517 (91%), Positives = 492/517 (95%)

Query: 1   MSVCAPNAVLSVSGIGKTYAQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAP 60
           MSVCAPNAVLSVSGIGKTYAQPVL GIDLTLMRGEVLALTGENGAGKSTLSKIIGGLV P
Sbjct: 1   MSVCAPNAVLSVSGIGKTYAQPVLAGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTP 60

Query: 61  TTGQMRFQGRDYRPGSRSQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSHGGWISRKQ 120
           TTGQM++QG+DYRPGSR+QAE LGIRMVMQELNLLPTLSVAENLFLDNLPS GGWISRKQ
Sbjct: 61  TTGQMQYQGQDYRPGSRAQAEALGIRMVMQELNLLPTLSVAENLFLDNLPSKGGWISRKQ 120

Query: 121 LRKAAIEAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTARE 180
           LRKAAIEAMA VGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTARE
Sbjct: 121 LRKAAIEAMAHVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTARE 180

Query: 181 VEMLFEQITRLQARGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTL 240
           VEMLFEQITRLQ+RGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTL
Sbjct: 181 VEMLFEQITRLQSRGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTL 240

Query: 241 MVGRELGEHIDMGPRKIGAPALTVKGLTRSDKVRDVSFEVRAGEIFGISGLIGAGRTELL 300
           MVGRELGEHIDMG RKIGAP LTV GL+RSDKVRDVSFEVRAGEIFGISGLIGAGRTELL
Sbjct: 241 MVGRELGEHIDMGARKIGAPVLTVNGLSRSDKVRDVSFEVRAGEIFGISGLIGAGRTELL 300

Query: 301 RLIFGADTADSGTVALGASAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIAL 360
           RLIFGAD ADSGT+ALGA AQV+++RSP DAVGHGIALITEDRKGEGLLLTQSI ANIAL
Sbjct: 301 RLIFGADIADSGTIALGAPAQVINVRSPVDAVGHGIALITEDRKGEGLLLTQSIGANIAL 360

Query: 361 GNMPVISSGGFVNNGDEMSLAQRQINAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDC 420
           GNMP IS  GFV+N  E +LAQRQI+AMRIRSS P QLVSELSGGNQQKVVIGRWLERDC
Sbjct: 361 GNMPGISGAGFVDNDKERALAQRQIDAMRIRSSGPAQLVSELSGGNQQKVVIGRWLERDC 420

Query: 421 TVMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLI 480
           +V+LFDEPTRGIDVGAKFDIY LLGELTRQGKALVVVSSDLRELMLICDRIGVLSAG LI
Sbjct: 421 SVLLFDEPTRGIDVGAKFDIYNLLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGSLI 480

Query: 481 DTFERDSWTQDDLLAAAFAGYQKRDALFNEAAPRDLP 517
           DTF+RDSWTQD+LLAAAFAGYQKRDA   EAAPRDLP
Sbjct: 481 DTFDRDSWTQDELLAAAFAGYQKRDAQLVEAAPRDLP 517


Lambda     K      H
   0.319    0.137    0.384 

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: 1008
Number of extensions: 34
Number of successful extensions: 5
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: 517
Length of database: 517
Length adjustment: 35
Effective length of query: 482
Effective length of database: 482
Effective search space:   232324
Effective search space used:   232324
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 (21.8 bits)
S2: 52 (24.6 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 paper from 2022 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