GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Pf6N2E2_5405 in Pseudomonas fluorescens GW456-L13

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate PfGW456L13_4773 Glutamate Aspartate transport ATP-binding protein GltL (TC 3.A.1.3.4)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5405
         (254 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4773 Glutamate
           Aspartate transport ATP-binding protein GltL (TC
           3.A.1.3.4)
          Length = 244

 Score =  285 bits (729), Expect = 6e-82
 Identities = 143/242 (59%), Positives = 179/242 (73%), Gaps = 2/242 (0%)

Query: 14  IIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVV 73
           +I ++ +NKWYG F VL D +  VK+GE IV+CGPSGSGKST I+C+N LE  Q+G IVV
Sbjct: 1   MISIKSINKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDIVV 60

Query: 74  DGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHY 133
           DG  + +    +  +R  VGMVFQHF LFPHLTI +N T+A + V    K +A +  +  
Sbjct: 61  DGTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGLQL 120

Query: 134 LERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMI 193
           LERV +   AHK+PGQLSGGQQQRVAIARAL M P +MLFDEPTSALDPEMV EVLD M+
Sbjct: 121 LERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMV 180

Query: 194 GLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFD--NPQNDRTKLFLSQ 251
            LA +GMTM+CVTHEMGFAR VA+RVIFMD+G+I+E     +FF   N + +RT+ FL++
Sbjct: 181 QLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARAERTQHFLNK 240

Query: 252 IL 253
           IL
Sbjct: 241 IL 242


Lambda     K      H
   0.322    0.137    0.407 

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: 212
Number of extensions: 4
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: 254
Length of database: 244
Length adjustment: 24
Effective length of query: 230
Effective length of database: 220
Effective search space:    50600
Effective search space used:    50600
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: 46 (22.3 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