GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Sphingomonas koreensis DSMZ 15582

Align Inositol transport system ATP-binding protein (characterized)
to candidate Ga0059261_0484 Ga0059261_0484 ABC-type multidrug transport system, ATPase component

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



>FitnessBrowser__Korea:Ga0059261_0484
          Length = 245

 Score =  100 bits (249), Expect = 3e-26
 Identities = 82/256 (32%), Positives = 119/256 (46%), Gaps = 17/256 (6%)

Query: 1   MSMSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPT 60
           M   Q  + +Q +   +G+   L G+++ V  G    LLG NGAGKST +  + G  +  
Sbjct: 1   MPQDQASVLLQDVSLAYGAQEVLRGLTLSVPAGSITALLGGNGAGKSTTLAALLGFVRAQ 60

Query: 61  KGDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFD 120
            G IL  G     +DP D     IA + +++A+   +S + N             L L  
Sbjct: 61  SGTILVCGVDPG-SDP-DGARRRIAYLPENVALYEHLSATENAEY---------LLALSG 109

Query: 121 HDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALG 180
             +A R   E     G+     DQ +G  S G RQ VAIA A+     VL+LDEPTS L 
Sbjct: 110 EQHARRDITEAFAAAGLQEEAWDQRLGGFSKGMRQKVAIAVALLRRVPVLLLDEPTSGLD 169

Query: 181 VRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTA-----QRGDI 235
            R TA+  A + +VR +G AV+ +TH++  A  V DR   L  G+          +R D+
Sbjct: 170 PRATADFNALVAQVRDRGTAVLMVTHDLLSAADVADRIAFLENGRVTDEVAASGPERFDV 229

Query: 236 SAEELQDMMAGGQELA 251
            A   +    GG+ LA
Sbjct: 230 RALHAR-FQVGGEPLA 244


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: 139
Number of extensions: 6
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: 245
Length adjustment: 24
Effective length of query: 237
Effective length of database: 221
Effective search space:    52377
Effective search space used:    52377
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