GapMind for catabolism of small carbon sources

 

Aligments for a candidate for H281DRAFT_01114 in Sinorhizobium meliloti 1021

Align deoxynucleoside transporter, substrate-binding component (characterized)
to candidate SM_b20316 SM_b20316 sugar ABC transporter substrate-binding protein

Query= reanno::Burk376:H281DRAFT_01114
         (334 letters)



>lcl|FitnessBrowser__Smeli:SM_b20316 SM_b20316 sugar ABC transporter
           substrate-binding protein
          Length = 333

 Score =  421 bits (1083), Expect = e-122
 Identities = 203/328 (61%), Positives = 251/328 (76%), Gaps = 4/328 (1%)

Query: 10  LAAAALTVGVIAAAQAATNE---TIVTVVKVTGINWFNRMDEGVKEFAKDNPGVTAYQTG 66
           +AA  + +G + AAQ A  +   ++VTVVKVTG NWF RM+EGV  + KDNP V+  Q G
Sbjct: 7   IAACTVALGALCAAQLAVAQDAPSVVTVVKVTGENWFTRMEEGVVAYGKDNPAVSTSQIG 66

Query: 67  PGRADAAQQLKIIEDLIAKKVNAIAVVPYDPPTLEPALKKAMDRGIKVVTHEADNAKNTM 126
           P +ADAAQQL++IEDL+AK VNAIAVVP DP  LE   K+AM+RGIK++THEAD+ KNT 
Sbjct: 67  PAKADAAQQLRLIEDLVAKNVNAIAVVPMDPSALEGVFKRAMNRGIKIITHEADSLKNTQ 126

Query: 127 VDIEAFDNTAYGAGLNERLASCMHNEGKWAVLVGSLGSRSQVQWADGGIGNAKAKYAKMN 186
           VDIEAFDN  +GA  NE+LA CM   GKW   VGSLGS + VQWADGG  NAK KY +M 
Sbjct: 127 VDIEAFDNKVFGARFNEKLAECMGKSGKWTSFVGSLGSLTHVQWADGGAENAK-KYPEME 185

Query: 187 LVEPKLETNNDGERAYEVAKEVLRKHPDLKGFQGSSSLDVIGIGRAVEEAGMQGKICVYG 246
           LV  K E+ ND  +AYE A+E+LRK+PD+KGFQG S++DVIGIGRAVEEAG+ GK+CV G
Sbjct: 186 LVSEKNESFNDANKAYEKAREILRKYPDIKGFQGGSAIDVIGIGRAVEEAGLVGKVCVVG 245

Query: 247 TGLPTEAGKFLESGAINGIAFWDPKLAGIAMNKVAKMLVDGKTVENGADLGIPGYTKVTV 306
            GLP +  K+LESGA+  I+FWDPK AG  MNKVA+++++GK + +G DLG+PGY KV+V
Sbjct: 246 LGLPKDTAKYLESGAVQSISFWDPKDAGYVMNKVAQLVIEGKEITDGMDLGVPGYNKVSV 305

Query: 307 AKGPGKGIIVRGQGWVNVDKSNYKQYPF 334
             GPG GIIV G+ WV+VDKSNY QYPF
Sbjct: 306 KNGPGDGIIVVGEAWVDVDKSNYSQYPF 333


Lambda     K      H
   0.314    0.133    0.385 

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: 412
Number of extensions: 13
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: 334
Length of database: 333
Length adjustment: 28
Effective length of query: 306
Effective length of database: 305
Effective search space:    93330
Effective search space used:    93330
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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