GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Dechlorosoma suillum PS

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Dsui_0629 Dsui_0629 branched-chain amino acid ABC-type transport system, permease component

Query= TCDB::P74318
         (286 letters)



>FitnessBrowser__PS:Dsui_0629
          Length = 307

 Score =  146 bits (369), Expect = 5e-40
 Identities = 96/302 (31%), Positives = 170/302 (56%), Gaps = 34/302 (11%)

Query: 5   QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTSGINLWLSMA 64
           Q I NG+ +GSI AL A+G T+ YGIL L NFAHG+ + + A       T+   + L   
Sbjct: 6   QQIINGLVLGSIYALVALGYTMVYGILGLINFAHGEVVMIGAL------TALTVVKLLAG 59

Query: 65  LGCVGTIIA-----------MFIG---EWLLWKPMRARRATATTLIIISIGLALFLRNGI 110
            G  G +IA           M IG   E + ++P+R  +A     +I +IG+++ L+N  
Sbjct: 60  SGLPGPVIALIGLMAAAPVCMAIGYGIEKIAYRPLR--KAPRLAPLITAIGVSIVLQNLA 117

Query: 111 LLIWGGNNQNYRVPIVPAQ--DFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMR 168
           +++WG +  ++   ++PA+  + +G  F   +++++ +A   M  L L++ RT++G+AMR
Sbjct: 118 MMVWGRSYHSFPA-VLPAEAHEVLGATFTDLQVIIVLVAAGMMAGLLLLINRTRLGRAMR 176

Query: 169 AVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKP-NMGWFLILPMFAS 227
           A A+N  +A++ G+NV  ++  T+V+ + L A+ G M     ++    MG+ L L  F +
Sbjct: 177 ATAENPAIAQLMGVNVNHIISLTFVIGSALAAVAGLMVSANYSIAHYYMGFILGLKAFTA 236

Query: 228 VILGGIGNPYGAIAGGIIIGVAQ--------EVSVPWFGTSYKMGVALLLMIIILFIRPQ 279
            +LGGIGN  GA+ GGI++G+ +        +++  + G+ Y+   A  ++I++L  RP 
Sbjct: 237 AVLGGIGNLAGAMIGGILLGLIESLGAGYIGDITGGFLGSHYQDVFAFFVLILVLVFRPS 296

Query: 280 GL 281
           GL
Sbjct: 297 GL 298


Lambda     K      H
   0.329    0.143    0.450 

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: 195
Number of extensions: 11
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: 286
Length of database: 307
Length adjustment: 26
Effective length of query: 260
Effective length of database: 281
Effective search space:    73060
Effective search space used:    73060
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 (21.8 bits)
S2: 48 (23.1 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