GapMind for catabolism of small carbon sources

 

Aligments for a candidate for frcB in Dinoroseobacter shibae DFL-12

Align Fructose import binding protein FrcB (characterized)
to candidate 3606963 Dshi_0390 periplasmic binding protein/LacI transcriptional regulator (RefSeq)

Query= SwissProt::Q9F9B2
         (341 letters)



>lcl|FitnessBrowser__Dino:3606963 Dshi_0390 periplasmic binding
           protein/LacI transcriptional regulator (RefSeq)
          Length = 337

 Score =  472 bits (1214), Expect = e-138
 Identities = 239/341 (70%), Positives = 273/341 (80%), Gaps = 4/341 (1%)

Query: 1   MKKTVLSAAFGALAMGVAFASPSQAAEVSACLITKTDTNPFFVKMKEGAAAKAKELGVTL 60
           MK  +L  A     M  A    + A   SACLITKTDTNPFFVKM+EGA AKA+ELGV L
Sbjct: 1   MKNLMLGTALACATMSGA----ALADTTSACLITKTDTNPFFVKMREGAVAKAEELGVEL 56

Query: 61  KSYAGKIDGDSESQVAAIETCIADGAKGILIAASDTQGIVPQVQKARDAGLLVIALDTPL 120
           K++AGK DGD E+QV AIETCI DGAKGILI ASDT  I   VQ+ARDAGL+VIALDTPL
Sbjct: 57  KTFAGKFDGDHETQVQAIETCILDGAKGILITASDTSSITGAVQQARDAGLVVIALDTPL 116

Query: 121 EPLDAADATFATDNLLAGKLIGQWAAATLGDAAKEAKVAFLDLTPSQPSVDVLRDQGFMI 180
            P DAADATFATDN +AG LIGQWA A +GDAA +AK+A L++  SQP+V VLR+QGF+ 
Sbjct: 117 TPADAADATFATDNYVAGLLIGQWARAQMGDAAADAKIAMLNIQVSQPTVGVLRNQGFLE 176

Query: 181 GFGIDPKDPNKIGDEDDPRIVGHDITNGNEEGGRTAMENLLQKDPTINVVHTINEPAAAG 240
           GFGID  DPN+ GDE DPRIVG D+T G+EEGGR AMEN+L  DP +NVV+TINEPAAAG
Sbjct: 177 GFGIDIGDPNRWGDETDPRIVGQDVTQGSEEGGRAAMENILAADPMVNVVYTINEPAAAG 236

Query: 241 AYEALKSVGREKDVLIVSVDGGCPGVKNVAEGVIGATSQQYPLMMAALGIEAIKKFADTG 300
           AYEALK++GRE DVLIVSVDGGCPGV+NVA+GVIGATSQQYPL+MA+LGIEAIK +A+TG
Sbjct: 237 AYEALKAIGRENDVLIVSVDGGCPGVQNVADGVIGATSQQYPLLMASLGIEAIKTWAETG 296

Query: 301 EKPTPTEGKDFVDTGVSLVADKPVSGVESIDTKTGMEKCWG 341
           EKP PT GKDF DTGV+LV D P  GVESI  + G   CWG
Sbjct: 297 EKPAPTPGKDFFDTGVALVTDTPADGVESISVEEGRNLCWG 337


Lambda     K      H
   0.313    0.132    0.372 

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: 487
Number of extensions: 16
Number of successful extensions: 1
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: 341
Length of database: 337
Length adjustment: 28
Effective length of query: 313
Effective length of database: 309
Effective search space:    96717
Effective search space used:    96717
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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