GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Magnetospirillum magneticum AMB-1

Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_011384429.1 AMB_RS10230 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF717
         (261 letters)



>NCBI__GCF_000009985.1:WP_011384429.1
          Length = 234

 Score =  114 bits (284), Expect = 2e-30
 Identities = 71/222 (31%), Positives = 115/222 (51%), Gaps = 10/222 (4%)

Query: 7   LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66
           ++ ++ ++ H+G   AL GVS+DV  GE   ++G NGAGK++ I+ ++G+ KP++G I F
Sbjct: 1   MLEVRDLDLHYGDAQALDGVSLDVAEGEVVAIIGANGAGKTSLIRAIAGMKKPSRGSIRF 60

Query: 67  EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANR 126
           EG  +           G+A V +   + P MSV  N  MG    R     K         
Sbjct: 61  EGHDIAGRASSRICDLGVAQVAEGRQIFPSMSVRENLEMGAVLPRARSKRK--------- 111

Query: 127 ITMEEMRKMGINLR-GPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTA 185
            T+E   +M   L+   DQA GTLSGGE+Q +AI R +    ++++ DEP+  L     +
Sbjct: 112 ETLERCYEMFPKLKVRSDQAAGTLSGGEQQMLAIGRCLMGQPRLMMFDEPSLGLAPAVVS 171

Query: 186 NVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTL 227
            +   I  +  +G+ V+ +  NV  +L + DR  VL  G+ +
Sbjct: 172 EMFKIIKTLHAEGMTVILVEQNVSASLKLADRGYVLENGRVV 213


Lambda     K      H
   0.321    0.137    0.395 

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: 158
Number of extensions: 7
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: 261
Length of database: 234
Length adjustment: 24
Effective length of query: 237
Effective length of database: 210
Effective search space:    49770
Effective search space used:    49770
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 (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:

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