GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Herbaspirillum seropedicae SmR1

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate HSERO_RS08275 HSERO_RS08275 branched-chain amino acid transporter permease subunit LivH

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__HerbieS:HSERO_RS08275
          Length = 308

 Score =  298 bits (763), Expect = 1e-85
 Identities = 148/300 (49%), Positives = 212/300 (70%), Gaps = 6/300 (2%)

Query: 6   QQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGLP 65
           QQL+NGL+LG+IY L+AIGYTMVYGIIGMINFAHG+I+M+  +  L+  L    + +G P
Sbjct: 10  QQLVNGLSLGAIYALIAIGYTMVYGIIGMINFAHGEIYMIASYVGLVT-LTAIGVQSGYP 68

Query: 66  VAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQGP 125
           + +LL   L+V++L+T L+ WT+ERVAYRPLRG  RL PLI+AIGMSI L N++Q+ QG 
Sbjct: 69  LPLLLGGALIVSVLVTGLYGWTVERVAYRPLRGGPRLVPLISAIGMSIFLQNYVQIGQGA 128

Query: 126 RNKPIPPMVSSVYQFG-----NISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATE 180
           R+  +P ++S   +F       +++   +++I+ +T VL+      + R+ +GRA RA  
Sbjct: 129 RDMSVPVLISGALEFQMGSDFTVTIPYSRMVIVGVTLVLMVALTLFIARSRMGRACRACA 188

Query: 181 QDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVL 240
           +D  MA LLG++ ++ IS TFV+GA LAAV G +  +  G  +   GF  G+KAFTAAVL
Sbjct: 189 EDMGMANLLGIDTNKVISFTFVLGAMLAAVGGVLIALTIGKLNPYIGFIAGIKAFTAAVL 248

Query: 241 GGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEVEKV 300
           GGIGS+PGA+ GG+L+GL E+  + Y    YKDV +F +L  +L+F+PTG+LG+P+VEKV
Sbjct: 249 GGIGSIPGAMLGGVLLGLAETFAAGYLPSEYKDVVSFGLLVLILLFRPTGLLGKPDVEKV 308


Lambda     K      H
   0.329    0.143    0.421 

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: 364
Number of extensions: 19
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: 300
Length of database: 308
Length adjustment: 27
Effective length of query: 273
Effective length of database: 281
Effective search space:    76713
Effective search space used:    76713
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