GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Phaeobacter inhibens BS107

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate GFF729 PGA1_c07440 ABC transporter, ATP binding protein

Query= reanno::Smeli:SMc03065
         (362 letters)



>FitnessBrowser__Phaeo:GFF729
          Length = 353

 Score =  327 bits (839), Expect = 2e-94
 Identities = 188/354 (53%), Positives = 230/354 (64%), Gaps = 9/354 (2%)

Query: 1   MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60
           MTG+ L    K YG V VIH +DL I +GEF VFVGPSGCGKSTLLRMIAGLEE + G++
Sbjct: 1   MTGVTLAKAVKKYGDVQVIHDVDLSIDDGEFCVFVGPSGCGKSTLLRMIAGLEETSSGNI 60

Query: 61  FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120
            I    V  +  + RG+AMVFQSYALYPHMTV DNM FG+++    KE+I  +V  A+ +
Sbjct: 61  HIGDRDVTRLDAADRGVAMVFQSYALYPHMTVEDNMGFGLKMNGHPKEKIREKVAEASRI 120

Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180
           L+L  YL R PKALSGGQRQRVAIGRAI R P+VFLFDEPLSNLDA LRV  R+EIA+L 
Sbjct: 121 LKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVDMRVEIARLH 180

Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240
           + +   TMIYVTHDQVEAMTLAD+IVVL AG +EQVG+P+ELY  P N FVA FIGSP+M
Sbjct: 181 KEIG-ATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGSPMELYANPDNRFVAGFIGSPSM 239

Query: 241 NVIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFEG 300
           N +  T+   G    V     + V   V   A  +G     G+RP+ L VT AD  L   
Sbjct: 240 NFLEGTVQGDG--VVVPALENRRVATSVALPA--DGSKVLLGLRPQHLSVTAADSSL--- 292

Query: 301 TVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFD 354
            + + E LG V+  Y+      E +I +  G   +  G  V    D A  ++FD
Sbjct: 293 VLDLRERLGGVSYDYL-STPTGEKLIVETRGDEALPEGTAVALGFDDADAYIFD 345


Lambda     K      H
   0.320    0.137    0.387 

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: 373
Number of extensions: 14
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: 362
Length of database: 353
Length adjustment: 29
Effective length of query: 333
Effective length of database: 324
Effective search space:   107892
Effective search space used:   107892
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 (21.8 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