GapMind for catabolism of small carbon sources

 

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

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AO353_20820 AO353_20820 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A166R419
         (517 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_20820
          Length = 517

 Score =  955 bits (2469), Expect = 0.0
 Identities = 493/517 (95%), Positives = 508/517 (98%)

Query: 1   MSVCAPNAVLSVSGIGKTYAQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAP 60
           MSVCAPNAVLSVSGIGKTYAQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLV P
Sbjct: 1   MSVCAPNAVLSVSGIGKTYAQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTP 60

Query: 61  TTGQMRFQGRDYRPGSRSQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSHGGWISRKQ 120
           TTGQM+FQGRDYRPGSR+QAEELGIRMVMQELNLLPTLSVAENLFLDNLPS+GGWISRKQ
Sbjct: 61  TTGQMQFQGRDYRPGSRTQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSNGGWISRKQ 120

Query: 121 LRKAAIEAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTARE 180
           LRKAAI AMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTARE
Sbjct: 121 LRKAAIAAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTARE 180

Query: 181 VEMLFEQITRLQARGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTL 240
           VEMLFEQITRLQARGV+IIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLV L
Sbjct: 181 VEMLFEQITRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVNL 240

Query: 241 MVGRELGEHIDMGPRKIGAPALTVKGLTRSDKVRDVSFEVRAGEIFGISGLIGAGRTELL 300
           MVGRELGEHID+GPR IGAPALTVKGL+RSDKVRDVSFEVR+GEIFGISGLIGAGRTELL
Sbjct: 241 MVGRELGEHIDLGPRHIGAPALTVKGLSRSDKVRDVSFEVRSGEIFGISGLIGAGRTELL 300

Query: 301 RLIFGADTADSGTVALGASAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIAL 360
           RLIFGAD ADSGTVALG+ AQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIAL
Sbjct: 301 RLIFGADAADSGTVALGSPAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIAL 360

Query: 361 GNMPVISSGGFVNNGDEMSLAQRQINAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDC 420
           GNMPVISSGG VN+GDEM+LAQRQI+AMRIRSSSP QLVSELSGGNQQKVVIGRWLER+C
Sbjct: 361 GNMPVISSGGIVNSGDEMALAQRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLEREC 420

Query: 421 TVMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLI 480
           +V+LFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLI
Sbjct: 421 SVLLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLI 480

Query: 481 DTFERDSWTQDDLLAAAFAGYQKRDALFNEAAPRDLP 517
           DTFERDSWTQDDLLAAAFAGYQKRDAL +EAAPRDLP
Sbjct: 481 DTFERDSWTQDDLLAAAFAGYQKRDALLHEAAPRDLP 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: 1031
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.

Links

Downloads

Related tools

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