GapMind for catabolism of small carbon sources

 

Aligments for a candidate for H281DRAFT_01115 in Herbaspirillum seropedicae SmR1

Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate HSERO_RS05100 HSERO_RS05100 sugar ABC transporter permease

Query= reanno::Burk376:H281DRAFT_01115
         (357 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05100 HSERO_RS05100 sugar ABC
           transporter permease
          Length = 337

 Score =  373 bits (958), Expect = e-108
 Identities = 190/312 (60%), Positives = 242/312 (77%), Gaps = 1/312 (0%)

Query: 12  ADRQLNFLLIVNVLVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALGIMLSMVSGNGG 71
           +D QL FLL++NV ++LVAT  S G F+DI N QSM  QLPELGLLA+G+ L+M+SGNGG
Sbjct: 8   SDPQLLFLLVINVAILLVATVFSHGDFLDIYNFQSMASQLPELGLLAIGVALAMISGNGG 67

Query: 72  IDLSGVGLANLSGMVAAMLVPRLVNGDDS-PVLYTSLFCAIVLMMGLLGGLLNGVVIARL 130
           IDLSG+GLANL+G+VAA  +P LV   D+ P  YT  F A+ L+ GLLGG LNG +I+R 
Sbjct: 68  IDLSGIGLANLAGVVAAAAMPLLVAAPDAAPWTYTLGFIAVALVTGLLGGALNGWLISRG 127

Query: 131 RLTPILCTLGTQLLFTGFAVVISNGASVHVDYVEPLSDIGNGTVLQVPIAFCIFLAAVIV 190
            LTPILCTLGTQ++FTG AVV++NG+S+ +  V+P+S IGN +VL VPI F IF+A +++
Sbjct: 128 NLTPILCTLGTQMIFTGLAVVLTNGSSLRISVVDPISAIGNESVLGVPIPFIIFVALLLL 187

Query: 191 LGWLLKRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISATHTSSA 250
           +GWL++ S FG++LYL+GTN +AA YAGI + R+   TY + GVLAS+AG+I A  T+S 
Sbjct: 188 VGWLMRYSLFGIKLYLLGTNARAARYAGISQNRLRFATYVISGVLASVAGIIIAARTASV 247

Query: 251 KWDYGNSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLLGVSQFFGDCA 310
           K DYGNSYLLIAILIAVM GV P GG+GR++C+FF+A  LQ LSS FNLL +S FF DCA
Sbjct: 248 KADYGNSYLLIAILIAVMAGVRPQGGYGRMVCLFFSALALQLLSSTFNLLEISNFFRDCA 307

Query: 311 WGFLLLLSLAFA 322
           WG LLL  LA A
Sbjct: 308 WGLLLLCFLASA 319


Lambda     K      H
   0.327    0.143    0.429 

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: 379
Number of extensions: 15
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: 357
Length of database: 337
Length adjustment: 29
Effective length of query: 328
Effective length of database: 308
Effective search space:   101024
Effective search space used:   101024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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 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