GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11885 in Rhizobium freirei PRF 81

Align Inositol transport system sugar-binding protein (characterized)
to candidate WP_004118879.1 RHSP_RS15695 ABC transporter substrate-binding protein

Query= reanno::WCS417:GFF2331
         (309 letters)



>NCBI__GCF_000359745.1:WP_004118879.1
          Length = 320

 Score =  112 bits (279), Expect = 2e-29
 Identities = 89/293 (30%), Positives = 146/293 (49%), Gaps = 18/293 (6%)

Query: 8   TALALSMLLASGV---ASAADLKIGVSMSAFDDTFLTYLREDMDKQAKSYPKGDGVQLQF 64
           TAL  + + A+ +   ASA  L +G S    +  +    R       K   K  G+ L+F
Sbjct: 5   TALISATIFAACMFTSASAKQLVVGFSQIGSESGW----RAAETTLTKQEAKKRGIDLKF 60

Query: 65  EDARADVVKQLSQVENFISQKVDAIIVNPVDTASTANIIKAATAAKIPLVFVNRRPDSQT 124
            DA+     Q+  + +FI+Q VDAI++ PV       ++K A  AKIP++ ++R  +   
Sbjct: 61  ADAQQKQENQIKAIRSFIAQGVDAILLAPVVETGWDAVLKEAKEAKIPVILLDRTVNGPK 120

Query: 125 LAPGVAAVTSDDVEAGKLQMQYIAEKLGGKG-NIVILLGDLANNSTTNRTKGVKEVLTKY 183
               + AVTSD V  GK+   ++ + +G K  NIV L G   ++    R KG +E +  +
Sbjct: 121 -DLYLTAVTSDLVHEGKVAGDWLVKTVGDKKCNIVELQGTTGSSPAIARKKGFEEAVKGH 179

Query: 184 PGIKIEQEQTGIWLRDRGMTLVNDWL---TQGRDFQAVLSNNDEMAIGAAMALKSAG--- 237
             +KI + QTG + R +G  ++  +L     G++  A+ ++ND+MA+GA  A+K AG   
Sbjct: 180 DNLKIVRSQTGDFTRAKGKEVMESFLKAENGGKNICALYAHNDDMAVGAIQAIKEAGLKP 239

Query: 238 KKGVLIAGVDGTPDGLNAITKGD--MTVSAFQDAKGQADKSVETARKMAKNEP 288
            K +L   +D  PD   A+  G+   TV    +  G A  +++   K  K EP
Sbjct: 240 GKDILTVSIDSVPDLFKAMAAGEANATVELTPNMAGPAFDALDAYLK-TKKEP 291


Lambda     K      H
   0.314    0.131    0.357 

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: 218
Number of extensions: 10
Number of successful extensions: 4
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: 309
Length of database: 320
Length adjustment: 27
Effective length of query: 282
Effective length of database: 293
Effective search space:    82626
Effective search space used:    82626
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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