GapMind for catabolism of small carbon sources

 

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

Align ATPase (characterized, see rationale)
to candidate PfGW456L13_4773 Glutamate Aspartate transport ATP-binding protein GltL (TC 3.A.1.3.4)

Query= uniprot:Q31RN8
         (261 letters)



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

 Score =  253 bits (645), Expect = 3e-72
 Identities = 130/243 (53%), Positives = 174/243 (71%), Gaps = 3/243 (1%)

Query: 21  MIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIW 80
           MI  + + KWYG+ FQ L   S  V++GEV+V+ GPSGSGKST ++ +NALE  Q+G+I 
Sbjct: 1   MISIKSINKWYGD-FQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDIV 59

Query: 81  IEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQ 140
           ++G  ++  + ++  +R  VGMVFQ F LFPHLT+ +NL +A ++V      +A     Q
Sbjct: 60  VDGTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGLQ 119

Query: 141 LLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVM 200
           LLERV ++  A K+PGQLSGGQQQRVAIARALAM P ++LFDEPTSALDPEMV EVLDVM
Sbjct: 120 LLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVM 179

Query: 201 RDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFF--TAPQSDRAKQFLA 258
             LA EGMTM+  THE+GFAR+VADRV+ M  G+I+E+   + FF     +++R + FL 
Sbjct: 180 VQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARAERTQHFLN 239

Query: 259 QIL 261
           +IL
Sbjct: 240 KIL 242


Lambda     K      H
   0.321    0.134    0.387 

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: 191
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: 261
Length of database: 244
Length adjustment: 24
Effective length of query: 237
Effective length of database: 220
Effective search space:    52140
Effective search space used:    52140
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, 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