GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltL in Pseudomonas stutzeri RCH2

Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate GFF16 Psest_0016 ectoine/hydroxyectoine ABC transporter, ATP-binding protein

Query= TCDB::P48243
         (242 letters)



>lcl|FitnessBrowser__psRCH2:GFF16 Psest_0016 ectoine/hydroxyectoine
           ABC transporter, ATP-binding protein
          Length = 278

 Score =  238 bits (608), Expect = 7e-68
 Identities = 125/251 (49%), Positives = 165/251 (65%), Gaps = 12/251 (4%)

Query: 1   MIKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEI 60
           +++  GV K +G+   L  +DL+I  G+ V ++GPSGSGKSTL R +  LE I+EG IE+
Sbjct: 24  LVRFAGVTKRYGELTVLDGLDLQIEEGEKVAIIGPSGSGKSTLLRVLMTLEGIDEGVIEV 83

Query: 61  DGKVL-----------PEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMK 109
           DG+ L           P   + L  +R  VGMVFQSFNLFPH+    NV  AP++V  + 
Sbjct: 84  DGEPLTHMPDASGQLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVMEAPVQVLGLS 143

Query: 110 KSEAEKLAMSLLERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDP 169
           K+EA   A  LL  VG+ ++ + +PAQLSGGQQQRVAIARALAM PK+MLFDE TSALDP
Sbjct: 144 KAEARGRAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLFDEVTSALDP 203

Query: 170 EMVNEVLDVMASLAK-EGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPK 228
           E+  EVL+V+  L +   +TM+ VTH+MGFAR+ ADRV F   G I E   PD  F NP+
Sbjct: 204 ELCGEVLNVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGSPDELFNNPQ 263

Query: 229 SDRAKDFLGKI 239
            +R ++FL  +
Sbjct: 264 EERTREFLSAV 274


Lambda     K      H
   0.319    0.135    0.379 

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: 211
Number of extensions: 6
Number of successful extensions: 3
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: 242
Length of database: 278
Length adjustment: 24
Effective length of query: 218
Effective length of database: 254
Effective search space:    55372
Effective search space used:    55372
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: 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, 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