GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00870 in Dechlorosoma suillum PS

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate Dsui_0630 Dsui_0630 ABC-type branched-chain amino acid transport system, periplasmic component

Query= uniprot:A0A165KTD4
         (375 letters)



>lcl|FitnessBrowser__PS:Dsui_0630 Dsui_0630 ABC-type branched-chain
           amino acid transport system, periplasmic component
          Length = 434

 Score =  425 bits (1092), Expect = e-123
 Identities = 214/358 (59%), Positives = 264/358 (73%), Gaps = 3/358 (0%)

Query: 14  AAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKIKFEL 73
           A AA  A+  E  VKIGH +P++G QAH GKDNE GA +AIEELNA+G+ IGG K+KFEL
Sbjct: 33  APAAAPAAKPEITVKIGHASPLTGPQAHIGKDNEYGATLAIEELNAKGLEIGGAKVKFEL 92

Query: 74  VAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAATNPNL 133
           +++DD ADPKQGT  AQK  DAKV GV+GHLNSGTTIPASK+Y D GIP ++G+ATNP  
Sbjct: 93  ISDDDQADPKQGTTVAQKFVDAKVNGVIGHLNSGTTIPASKIYFDAGIPQISGSATNPTY 152

Query: 134 TKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKTATAKG 193
           TK G+ T FR++AND   G  LA +A  TL  K+VAIIDDRTAYGQG+AD FKK A A G
Sbjct: 153 TKQGFATAFRVMANDEQQGKALAQFAAKTLAAKSVAIIDDRTAYGQGLADEFKKAAEAAG 212

Query: 194 MKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVKYFGG 253
           +KVV  ++T DKATDF AILT IK+K PD IFYGGMDPQGGPM +QM++LG+   K+  G
Sbjct: 213 LKVVASEYTNDKATDFKAILTKIKSKKPDLIFYGGMDPQGGPMAKQMKELGL-KAKFLTG 271

Query: 254 DGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYSPYTYD 313
           DG CT     L AGA   G   C+  G  L KMPGGT +K K+  K+  + Q+Y+PY YD
Sbjct: 272 DGGCTPNFITL-AGAAAEGQ-YCSLPGVPLDKMPGGTVFKDKFVGKFKTEIQLYAPYVYD 329

Query: 314 ATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVYKDGK 371
           AT ++VDAMKRANSV+P  Y PE+ K+SF+GVT+ I F+  G++K+ AI+ Y YK GK
Sbjct: 330 ATMVLVDAMKRANSVEPAKYLPEIGKTSFQGVTAKIGFDEFGDLKDGAISFYEYKGGK 387


Lambda     K      H
   0.315    0.131    0.375 

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: 551
Number of extensions: 22
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: 375
Length of database: 434
Length adjustment: 31
Effective length of query: 344
Effective length of database: 403
Effective search space:   138632
Effective search space used:   138632
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: 50 (23.9 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