GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Sinorhizobium meliloti 1021

Align Inositol transport system ATP-binding protein (characterized)
to candidate SMa0216 SMa0216 ABC transporter ATP-binding protein

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



>FitnessBrowser__Smeli:SMa0216
          Length = 246

 Score =  184 bits (467), Expect = 2e-51
 Identities = 101/242 (41%), Positives = 150/242 (61%), Gaps = 4/242 (1%)

Query: 3   MSQP-LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTK 61
           MS P L+ +  I K FG++ AL  +S  +  GE   LLGDNGAGKST +  +SG+HKPT 
Sbjct: 2   MSTPNLLELHNISKSFGALTALRNLSFHIGEGEVVGLLGDNGAGKSTTVNLISGIHKPTD 61

Query: 62  GDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFD- 120
           G +  +G+   F+   D+  AGI T++QH A++  +S++RN FMG E   + G L+  + 
Sbjct: 62  GYLSVDGKKTTFSCRSDSADAGIETIYQHTALVDSLSITRNIFMGRELTDRFGFLRQREM 121

Query: 121 HDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALG 180
            D A  +    +   GI+   PD  VG LSGG++Q VAIARAV+F  +VL+LDEPTSAL 
Sbjct: 122 RDIAMEVLQNAVHISGID--SPDTLVGNLSGGQKQAVAIARAVYFKKRVLLLDEPTSALS 179

Query: 181 VRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEEL 240
           VR+T  +L  + K++ + V+ V +THN+ HA  V DRF +++ G  +   Q+ D +  +L
Sbjct: 180 VRETEALLNQVLKLKAENVSSVLVTHNLYHAYQVCDRFVIMSHGTKVFDVQKADTTISQL 239

Query: 241 QD 242
            +
Sbjct: 240 TE 241


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: 151
Number of extensions: 8
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 261
Length of database: 246
Length adjustment: 24
Effective length of query: 237
Effective length of database: 222
Effective search space:    52614
Effective search space used:    52614
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