GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Herbaspirillum seropedicae SmR1

Align GtsC (GLcG), component of Glucose porter, GtsABCD (characterized)
to candidate HSERO_RS01335 HSERO_RS01335 sugar ABC transporter permease

Query= TCDB::Q88P36
         (281 letters)



>FitnessBrowser__HerbieS:HSERO_RS01335
          Length = 283

 Score =  178 bits (451), Expect = 1e-49
 Identities = 94/274 (34%), Positives = 162/274 (59%), Gaps = 6/274 (2%)

Query: 12  LSRMAIHAVLLIAVLLYLVPLVVMLLTSFKTPEDITTGNLLSWP---AVITGIGWVKAWG 68
           ++R    A L +A+L++L+P++  L+TS ++ +++  GN   WP   A++          
Sbjct: 12  INRALYRASLPVALLIWLLPMLAALVTSIRSNDELMAGNYWGWPQDFAMLENYREALTAS 71

Query: 69  AVSGYFWNSIMITVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLP 128
            +  YFWNS +IT+P+V+ + ++ A+ G+ LS ++FRG+ + F   +   F+P Q +++P
Sbjct: 72  PMLHYFWNSCLITIPSVIGAISLAAMAGFALSTYQFRGNTVLFATFVACNFVPQQILMIP 131

Query: 129 ASFTLGKLGLASTTGGLVLVHVVYGLAFTTLFFRNFYVSIPDALVKAARLDGAGFFTIFR 188
                  LGL +T  G++L H+     F TLF RNF   +P  +++AAR++GA  +T+F 
Sbjct: 132 VRDLSLSLGLFNTITGMMLFHIAMQTGFCTLFLRNFIKQLPFEMIEAARIEGASEWTVFY 191

Query: 189 RIILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDS-QPITVALNNLVNTSTGAKEYNV 247
           RI+LP+  P +    +  FT +WND+ + +V + GD   PITV +  L    T A  +N+
Sbjct: 192 RIVLPLIRPALAALAVLVFTFVWNDYFWALVLTQGDDVAPITVGVAALRGQWTTA--WNL 249

Query: 248 DMAAAMIAGLPTLLVYVVAGKYFVRGLTAGAVKG 281
             A +++A LP+++++ V  K FV GLT GA KG
Sbjct: 250 VSAGSILAALPSVILFFVMQKQFVAGLTFGASKG 283


Lambda     K      H
   0.329    0.142    0.443 

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: 225
Number of extensions: 13
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: 281
Length of database: 283
Length adjustment: 26
Effective length of query: 255
Effective length of database: 257
Effective search space:    65535
Effective search space used:    65535
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: 47 (22.7 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