GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Pseudomonas litoralis 2SM5

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_090272110.1 BLU11_RS03765 high-affinity branched-chain amino acid ABC transporter permease LivH

Query= TCDB::P74318
         (286 letters)



>NCBI__GCF_900105005.1:WP_090272110.1
          Length = 308

 Score =  142 bits (358), Expect = 9e-39
 Identities = 88/295 (29%), Positives = 160/295 (54%), Gaps = 19/295 (6%)

Query: 3   LSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTSGINLWL- 61
           L Q + NG+ VGS  AL A+G T+ YGI+ + NFAHG+   + +Y+ +    +   L + 
Sbjct: 8   LLQQLLNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIVLAALALLGIE 67

Query: 62  SMALGCVGTIIAMFIG--------EWLLWKPMRARRATATTLIIISIGLALFLRNGILLI 113
           S+ L  +  ++   I         E + ++P+R         +I +IG+++FL+N + L 
Sbjct: 68  SLPLLIIAALVVSMIVTSAYGYSIERVAYRPLRGGNRLIP--LISAIGMSIFLQNLVRLA 125

Query: 114 WGG------NNQNYRVPIVPAQDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAM 167
            G       N     + I PA  F      Y ++++  + + +M +L L + R+++G+A 
Sbjct: 126 QGSRDIAMPNLVRGGIDIGPATGFHAT-LSYMQIIIFVVTLISMTLLTLFITRSRMGRAC 184

Query: 168 RAVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMT-TLKPNMGWFLILPMFA 226
           RA A+++ +  + GIN   ++  T+++ A L A+ G + G+    + P +G+   L  F 
Sbjct: 185 RACAEDLKMTNLLGINTNSIIALTFIIGAALAAVAGVLLGMYYGVINPYIGFMAGLKAFT 244

Query: 227 SVILGGIGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGL 281
           + +LGGIG+  GA+ GG+++GVA+ ++  +F   YK  VA  L+I+IL  RP G+
Sbjct: 245 AAVLGGIGSIPGAVLGGLLLGVAEAMTAGYFSGEYKDVVAFSLLILILLFRPSGI 299


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: 205
Number of extensions: 11
Number of successful extensions: 4
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: 308
Length adjustment: 26
Effective length of query: 260
Effective length of database: 282
Effective search space:    73320
Effective search space used:    73320
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 24 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