GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Nocardiopsis baichengensis YIM 90130

Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_017556214.1 C892_RS0104280 urea ABC transporter permease subunit UrtB

Query= TCDB::P21627
         (307 letters)



>NCBI__GCF_000341205.1:WP_017556214.1
          Length = 294

 Score =  129 bits (325), Expect = 6e-35
 Identities = 96/291 (32%), Positives = 144/291 (49%), Gaps = 10/291 (3%)

Query: 8   LQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDS 67
           L QL     VG+   L A+G    +G +G+IN AHGE  M+G+Y AF A+   A +G  +
Sbjct: 5   LAQLPIAAAVGAVLLLAALGLNFTFGQMGVINMAHGEFLMVGAYTAF-ALQAWAGLGGGA 63

Query: 68  VPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQDS 127
           V L + AAFA    +T+  G ++ER   R   G   L  L+   G+S+ LQ    L++D 
Sbjct: 64  VLLALPAAFA----LTALMGLALERGLIRHFYG-RPLDTLLLTFGVSLVLQQ---LARDV 115

Query: 128 KEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRACA 187
                  +    ++ G + + GV + + ++ I  +  L +  + L+I RSR GR  RA  
Sbjct: 116 FGAPNVDVTAPAWLAGGTRVLGVWLHHSRLFIIALAALAVVAIALYIGRSRSGRYMRAVL 175

Query: 188 EDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAAVL 247
            D  +  + GI    + A TF +G+ LA VA V L +  G I P IG    + AF   V+
Sbjct: 176 HDRDLAAVSGIPVGRVDAATFAVGSGLAGVAGVALAL-IGPIGPSIGTSYIVDAFLVVVV 234

Query: 248 GGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGI 298
           GG+GS+ GA++    LG   A+           VV F  +I  L  RP G+
Sbjct: 235 GGLGSLRGAVVAAFGLGALNAYSELWTDASLAKVVVFAAIIAFLQARPQGL 285


Lambda     K      H
   0.328    0.145    0.413 

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: 252
Number of extensions: 19
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: 307
Length of database: 294
Length adjustment: 27
Effective length of query: 280
Effective length of database: 267
Effective search space:    74760
Effective search space used:    74760
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: 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