GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcB in Rhodobacter viridis JA737

Align Fructose import binding protein FrcB (characterized)
to candidate WP_110804308.1 C8J30_RS03215 sugar ABC transporter substrate-binding protein

Query= SwissProt::Q9F9B2
         (341 letters)



>NCBI__GCF_003217355.1:WP_110804308.1
          Length = 338

 Score =  481 bits (1239), Expect = e-141
 Identities = 243/334 (72%), Positives = 273/334 (81%)

Query: 8   AAFGALAMGVAFASPSQAAEVSACLITKTDTNPFFVKMKEGAAAKAKELGVTLKSYAGKI 67
           A  GA A+ +   +    AE  ACLITKTDTNPFFVKMKEGA A+A++LG+TLKSYAGK+
Sbjct: 5   ALLGASAVAMTALAGGAFAETGACLITKTDTNPFFVKMKEGAQAEAEKLGITLKSYAGKV 64

Query: 68  DGDSESQVAAIETCIADGAKGILIAASDTQGIVPQVQKARDAGLLVIALDTPLEPLDAAD 127
           DGD+E+QVAAIETCIADGAKGILI  SDT+ IVP VQKAR+AG+LVIALDTPL+P+DAAD
Sbjct: 65  DGDNEAQVAAIETCIADGAKGILITPSDTKAIVPTVQKAREAGILVIALDTPLDPMDAAD 124

Query: 128 ATFATDNLLAGKLIGQWAAATLGDAAKEAKVAFLDLTPSQPSVDVLRDQGFMIGFGIDPK 187
            TFATDN  AG LIGQWA A LGDAA  AK+A LDL  SQP+VDVLRDQGF+ GFGID  
Sbjct: 125 MTFATDNFSAGLLIGQWAKANLGDAAANAKIAMLDLAVSQPTVDVLRDQGFLQGFGIDLG 184

Query: 188 DPNKIGDEDDPRIVGHDITNGNEEGGRTAMENLLQKDPTINVVHTINEPAAAGAYEALKS 247
           D NK GDE D RIVGHD+T GNEEGGR AMENLL KDP INVV+TINEPAAAGAYEALK+
Sbjct: 185 DANKWGDETDARIVGHDVTAGNEEGGRKAMENLLAKDPDINVVYTINEPAAAGAYEALKA 244

Query: 248 VGREKDVLIVSVDGGCPGVKNVAEGVIGATSQQYPLMMAALGIEAIKKFADTGEKPTPTE 307
           VG+++  LIVSVDGGCPGVKNV  GVIGATSQQYP++MA+ GIEAI  FA  G KP  TE
Sbjct: 245 VGKDQGTLIVSVDGGCPGVKNVEGGVIGATSQQYPMLMASKGIEAIAAFAKDGTKPAATE 304

Query: 308 GKDFVDTGVSLVADKPVSGVESIDTKTGMEKCWG 341
           GK F DTGV L+ DKPV GV SID+K G+  CWG
Sbjct: 305 GKTFFDTGVQLITDKPVEGVPSIDSKAGLGICWG 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: 483
Number of extensions: 19
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 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