GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Pf6N2E2_5405 in Synechococcus elongatus PCC 7942

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate Synpcc7942_0249 Synpcc7942_0249 ATPase

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



>lcl|FitnessBrowser__SynE:Synpcc7942_0249 Synpcc7942_0249 ATPase
          Length = 261

 Score =  306 bits (783), Expect = 4e-88
 Identities = 156/245 (63%), Positives = 190/245 (77%), Gaps = 1/245 (0%)

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

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

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

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

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


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: 233
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: 254
Length of database: 261
Length adjustment: 24
Effective length of query: 230
Effective length of database: 237
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.

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 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