GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braD in Herbaspirillum seropedicae SmR1

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 HSERO_RS08275 HSERO_RS08275 branched-chain amino acid transporter permease subunit LivH

Query= TCDB::P21627
         (307 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS08275 HSERO_RS08275
           branched-chain amino acid transporter permease subunit
           LivH
          Length = 308

 Score =  374 bits (959), Expect = e-108
 Identities = 184/299 (61%), Positives = 236/299 (78%)

Query: 9   QQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDSV 68
           QQLVNGL++G+ YALIAIGYTMVYGIIGMINFAHGE+YMI SY+  + +T + +     +
Sbjct: 10  QQLVNGLSLGAIYALIAIGYTMVYGIIGMINFAHGEIYMIASYVGLVTLTAIGVQSGYPL 69

Query: 69  PLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQDSK 128
           PL++  A   S++VT  +G+++ERVAYRPLRGG RL+PLISAIGMSIFLQN V + Q ++
Sbjct: 70  PLLLGGALIVSVLVTGLYGWTVERVAYRPLRGGPRLVPLISAIGMSIFLQNYVQIGQGAR 129

Query: 129 EKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRACAE 188
           + ++P L+ G   F   S   V I Y +++I  VT ++M  LTLFI+RSR+GRACRACAE
Sbjct: 130 DMSVPVLISGALEFQMGSDFTVTIPYSRMVIVGVTLVLMVALTLFIARSRMGRACRACAE 189

Query: 189 DLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAAVLG 248
           D+ M NLLGI++N +I+ TFV+GA LAAV  VL+ +  G +NP IGF+AGIKAFTAAVLG
Sbjct: 190 DMGMANLLGIDTNKVISFTFVLGAMLAAVGGVLIALTIGKLNPYIGFIAGIKAFTAAVLG 249

Query: 249 GIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEVEKV 307
           GIGSIPGAMLGG+LLG+AE F A     +YKDVV+FGLL+L+LLFRPTG+LG+P+VEKV
Sbjct: 250 GIGSIPGAMLGGVLLGLAETFAAGYLPSEYKDVVSFGLLVLILLFRPTGLLGKPDVEKV 308


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: 380
Number of extensions: 10
Number of successful extensions: 2
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: 308
Length adjustment: 27
Effective length of query: 280
Effective length of database: 281
Effective search space:    78680
Effective search space used:    78680
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 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 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, the preprint on GapMind for carbon sources, 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