GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacF in Rhizobium freirei PRF 81

Align ABC transporter for Lactose, permease component 1 (characterized)
to candidate WP_037152420.1 RHSP_RS16215 sugar ABC transporter permease

Query= reanno::Smeli:SM_b21653
         (298 letters)



>NCBI__GCF_000359745.1:WP_037152420.1
          Length = 305

 Score =  155 bits (391), Expect = 1e-42
 Identities = 95/282 (33%), Positives = 152/282 (53%), Gaps = 6/282 (2%)

Query: 10  RYYDVNGWLFVAPALGLITLFMVYPIAWSLWMSFQSGRGM-TLKFAGFANIVRLWNDPVF 68
           R+   +G+L++APA+ L+ +F V P+ +++WMSF +   +   ++ GF N +R+++D  F
Sbjct: 17  RHAGWHGFLYIAPAMALVIVFFVLPVVFTVWMSFHNWPLLGNPRWIGFGNYIRMFSDMRF 76

Query: 69  IKALTNTMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLPCVSSLVAYSVLFK 128
           + AL  T  Y VV    +  +A  LA  +   +    G++RT IFLP V  L   S+L+ 
Sbjct: 77  MAALRFTAYYTVVVTIAIFAVAFPLAFFVEKHKPFV-GLYRTVIFLPVVIGLATASLLWV 135

Query: 129 GMFATD-GIVNSTLQAIGLAASPIPWLTHPFWAKVLVILAITWRWTGYNMIFYLAALQNI 187
            +   D G       A+GL       L     A   +I+ + W+  G+ MI  L  LQ I
Sbjct: 136 WLANVDSGFFAPIALALGLVDKRPNLLADFDMAFATIIVMVVWKIAGFTMIILLTGLQAI 195

Query: 188 DKSIYEVARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGTLQLFDEVYNLTEGKGGPS 247
              + E ARIDG   W R  HLT+PL++  I    +IS  G++  FD+ Y +T   GGP 
Sbjct: 196 PSELTEAARIDGARRWQRFRHLTLPLMRRTIALALIISITGSVLAFDQFYIMT--SGGPQ 253

Query: 248 NATLTLSLYIYNLTFRFMPNLGYAATVSYVIVVLVALLAFVQ 289
           N  +++  YI+N +F    NLGY A +S  ++V++ L++ VQ
Sbjct: 254 NRMISVVYYIFNQSFVSF-NLGYGAALSIALLVILVLISVVQ 294


Lambda     K      H
   0.330    0.142    0.447 

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: 238
Number of extensions: 11
Number of successful extensions: 5
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: 298
Length of database: 305
Length adjustment: 27
Effective length of query: 271
Effective length of database: 278
Effective search space:    75338
Effective search space used:    75338
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 (21.9 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