GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bgtA in Pseudomonas fluorescens FW300-N2E3

Align ATPase (characterized, see rationale)
to candidate AO353_04600 AO353_04600 glutamine ABC transporter ATP-binding protein

Query= uniprot:Q31RN8
         (261 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_04600 AO353_04600 glutamine
           ABC transporter ATP-binding protein
          Length = 254

 Score =  304 bits (779), Expect = 1e-87
 Identities = 155/245 (63%), Positives = 190/245 (77%), Gaps = 1/245 (0%)

Query: 17  APETMIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQR 76
           +PE +I  +GV KWYG QF  L  ++L V++GE +V+ GPSGSGKST +R LN LE HQ+
Sbjct: 10  SPEGIIQMQGVNKWYG-QFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQ 68

Query: 77  GEIWIEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEA 136
           G I ++G  L++D + I  IR+EVGMVFQ FNLFPHLT+LQN  LAP+ VR+ P  +AE 
Sbjct: 69  GRIVVDGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEE 128

Query: 137 TARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREV 196
            A   LERVRI EQA KYPGQLSGGQQQRVAIARAL M+P+I+LFDEPTSALDPEMV+EV
Sbjct: 129 IAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEV 188

Query: 197 LDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQF 256
           LD M  LA +GMTML  THE+GFAR VA+RV+ M  G+IVE+A P+ FF  PQ++R K F
Sbjct: 189 LDTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNERTKLF 248

Query: 257 LAQIL 261
           L+QIL
Sbjct: 249 LSQIL 253


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: 228
Number of extensions: 4
Number of successful extensions: 2
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: 254
Length adjustment: 24
Effective length of query: 237
Effective length of database: 230
Effective search space:    54510
Effective search space used:    54510
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: 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 (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