GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglB in Dyella japonica UNC79MFTsu3.2

Align glucose transporter, periplasmic substrate-binding component (characterized)
to candidate N515DRAFT_3231 N515DRAFT_3231 xylose-binding protein

Query= reanno::Phaeo:GFF3639
         (341 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3231
          Length = 341

 Score =  212 bits (540), Expect = 1e-59
 Identities = 123/331 (37%), Positives = 192/331 (58%), Gaps = 14/331 (4%)

Query: 5   SGVSALAFAATASMAFAEDVTVGVSWSNFQEERWKTDEAAIKAALEAKGATYVSADAQSS 64
           +G++  A  A +  A ++   +G S  + + ERW  D     AA E  GA      A  +
Sbjct: 15  TGLAVAALTACSGKA-SDQPKIGFSIDDMRLERWTRDRDYFVAAAEKLGAKVYVQSADGN 73

Query: 65  SAKQLSDIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGRA-FYLT 123
             +Q+  +E+LI++GV+ L+++  +++ +   +  A   GI V++YDRLI       Y++
Sbjct: 74  EQRQVQQLENLISRGVNVLVIVPFNSKVLDNVIAEAKRNGIKVISYDRLILGADVDAYIS 133

Query: 124 FDNVEVGRMQARAVLEAQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKIVGE 183
           FDN +VG +QA+ VL+A P GNY ++ GSPTD NA  LR GQ +++Q AID GD+KIVG+
Sbjct: 134 FDNEKVGELQAQGVLDAVPKGNYFLLGGSPTDNNAKILREGQLKVLQPAIDRGDVKIVGQ 193

Query: 184 AYTDGWLPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAALTAQGMEG-IAVSGQDG 242
            +T  W  + A R +E  LTAN N +  +VASND TAGG + AL AQ + G +AVSGQD 
Sbjct: 194 QWTPEWDASKALRIVEDALTANHNDIQGIVASNDATAGGAIQALAAQQLAGKVAVSGQDA 253

Query: 243 DHAALNRVAKGTQTVSVWKDARDLGKAAANIAVEMAEG---AVMGDVAGGAAWTSPAGTE 299
           D A + RV  GTQ ++V+K  + +   AA +AV++A+G      G +  G         +
Sbjct: 254 DLAGVRRVVDGTQAMTVYKPLKTIATTAAELAVKLAKGEAPTYTGKMNNGK-------KD 306

Query: 300 LTARFLEPIPVTADNL-SVVVDAGWITKEAL 329
           + +  L+P  +T D +   V+  G+ T+E +
Sbjct: 307 VDSVLLQPTLLTKDKVDDTVIKDGFYTREQI 337


Lambda     K      H
   0.313    0.128    0.362 

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: 234
Number of extensions: 5
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: 341
Length of database: 341
Length adjustment: 29
Effective length of query: 312
Effective length of database: 312
Effective search space:    97344
Effective search space used:    97344
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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