GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2396 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)



>FitnessBrowser__PS:Dsui_0630
          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.

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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