GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Herbaspirillum seropedicae SmR1

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate HSERO_RS08920 HSERO_RS08920 ABC transporter

Query= TCDB::Q8DQH9
         (318 letters)



>FitnessBrowser__HerbieS:HSERO_RS08920
          Length = 655

 Score =  146 bits (368), Expect = 2e-39
 Identities = 98/290 (33%), Positives = 158/290 (54%), Gaps = 16/290 (5%)

Query: 12  LLLLLAGYSLISVLVSVGVLNLFYVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMA 71
           LLL L G   ++ +  V V N +Y+ +++ I I  IL  GL+++VG++GQ SLGHAG   
Sbjct: 6   LLLSLLGIVALAGIPMV-VHNPYYLHLIETILIYAILLFGLDIVVGYTGQVSLGHAGLFG 64

Query: 72  IGAYAAAIIGSK--SPTYGAFFGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSE 129
           IG+YAA ++  K   P +     A+ V A+    +AL    P LR+ G YLA+ TL    
Sbjct: 65  IGSYAAGVLFFKLGMPIFVTVPAAIAVTAVFGAILAL----PALRVTGPYLAMVTLAFGT 120

Query: 130 IIRIFIINGGSLTNGAAGI------LGIPNFTTWQMVYFFVVITTIATL---NFLRSPIG 180
           II+I I     LT G  GI      +G    +  Q  Y   V+  ++ L     L+S +G
Sbjct: 121 IIQILINEMTFLTEGPLGIKLQKPMIGGDKMSEVQFFYLVAVLMVLSMLVVHRILKSNLG 180

Query: 181 RSTLSVREDEIAAESVGVNTTKIKIIAFVFGAITASIAGSLQAGFIGSVVPKDYTFINSI 240
           R+  ++R+  IA++ +GV+  + K+ AF+  A  A ++G+L A     + P  Y F  +I
Sbjct: 181 RAFQALRDSPIASDCMGVSVYRYKVYAFIISAALAGLSGALYAYSEEYISPNTYNFELTI 240

Query: 241 NVLIIVVFGGLGSITGAIVSAIVLGILNMLLQDVASVRMIIYALALVLVM 290
             L+ V+ GG  S  G+++ A+++ +L  LL D+A  R I   LA+++V+
Sbjct: 241 MFLLAVIMGGRKSRIGSLIGALIVVMLPSLLSDIALFRQIATVLAVIVVV 290


Lambda     K      H
   0.327    0.143    0.403 

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: 348
Number of extensions: 16
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: 318
Length of database: 655
Length adjustment: 33
Effective length of query: 285
Effective length of database: 622
Effective search space:   177270
Effective search space used:   177270
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 (21.6 bits)
S2: 51 (24.3 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