GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcB in Phaeobacter inhibens BS107

Align Fructose import binding protein FrcB (characterized)
to candidate GFF2763 PGA1_c28060 putative sugar transport system, periplasmic protein

Query= SwissProt::Q9F9B2
         (341 letters)



>FitnessBrowser__Phaeo:GFF2763
          Length = 338

 Score =  500 bits (1287), Expect = e-146
 Identities = 257/342 (75%), Positives = 286/342 (83%), Gaps = 5/342 (1%)

Query: 1   MKKTVLSAAFGALAM-GVAFASPSQAAEVSACLITKTDTNPFFVKMKEGAAAKAKELGVT 59
           MKK +L  A G  AM G AFA    A  V+ACLITKTDTNPFFVKMKEGA AKA ELG+T
Sbjct: 1   MKKLLLGTAIGFAAMTGSAFA----AEGVTACLITKTDTNPFFVKMKEGAEAKAAELGMT 56

Query: 60  LKSYAGKIDGDSESQVAAIETCIADGAKGILIAASDTQGIVPQVQKARDAGLLVIALDTP 119
           LKS+AGK+DGD E+QVAAIETCIADGAKGIL+ ASDT  IVP VQ+ARDAGL+VIALDTP
Sbjct: 57  LKSFAGKVDGDHETQVAAIETCIADGAKGILLTASDTSSIVPAVQQARDAGLVVIALDTP 116

Query: 120 LEPLDAADATFATDNLLAGKLIGQWAAATLGDAAKEAKVAFLDLTPSQPSVDVLRDQGFM 179
           LEP+D+ADATFATDN LAG+LIG+WAAA+LGD A  AK+A LDL  SQP+V VLRDQGF+
Sbjct: 117 LEPIDSADATFATDNFLAGELIGKWAAASLGDEAANAKIAMLDLAVSQPTVGVLRDQGFL 176

Query: 180 IGFGIDPKDPNKIGDEDDPRIVGHDITNGNEEGGRTAMENLLQKDPTINVVHTINEPAAA 239
            GFGID  DPNK GDE DPRIVG+DIT GNEEGGR AMENLL KDP INVV+TINEPAAA
Sbjct: 177 QGFGIDLGDPNKWGDETDPRIVGNDITAGNEEGGRRAMENLLAKDPMINVVYTINEPAAA 236

Query: 240 GAYEALKSVGREKDVLIVSVDGGCPGVKNVAEGVIGATSQQYPLMMAALGIEAIKKFADT 299
           GAYEALKS+GRE DVLIVSVDGGCPGV+N+ +GVIGATSQQYPL+MA+ GIEAI  +A T
Sbjct: 237 GAYEALKSIGRENDVLIVSVDGGCPGVQNIKDGVIGATSQQYPLLMASKGIEAISAWATT 296

Query: 300 GEKPTPTEGKDFVDTGVSLVADKPVSGVESIDTKTGMEKCWG 341
           GEKP PT GK F DTGV+LV D+P  GV+SIDT  G   CWG
Sbjct: 297 GEKPAPTPGKAFFDTGVALVTDQPAEGVDSIDTAEGTNLCWG 338


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: 488
Number of extensions: 17
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: 338
Length adjustment: 28
Effective length of query: 313
Effective length of database: 310
Effective search space:    97030
Effective search space used:    97030
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:

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