GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Rhodobacter johrii JA192

Align Fructose import permease protein FrcC (characterized)
to candidate WP_108223269.1 C8J29_RS11820 ABC transporter permease

Query= SwissProt::Q9F9B1
         (360 letters)



>NCBI__GCF_003046325.1:WP_108223269.1
          Length = 363

 Score =  522 bits (1345), Expect = e-153
 Identities = 267/362 (73%), Positives = 306/362 (84%), Gaps = 8/362 (2%)

Query: 6   TAAQPSQEFEKVLADSSTDVASFDAHDKTLLQKLQHFLHSSPAAVPLIVLVLSLIAFGVI 65
           T     Q FE  L  S   VA F+   ++ +Q+ +H LH +P+ VPLIVLV+S+  FG +
Sbjct: 3   TETHGPQGFEAALNRSPDSVAEFEQR-RSFVQQARHLLHQTPSLVPLIVLVVSVSIFGAL 61

Query: 66  LGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMVLSSVIMGQFTFRYG 125
           LG KFFSAFT+TLILQQVAIVGIVGAAQTLV+LTAGIDLSVGAIMVLSSVIMGQFTFRYG
Sbjct: 62  LGQKFFSAFTLTLILQQVAIVGIVGAAQTLVVLTAGIDLSVGAIMVLSSVIMGQFTFRYG 121

Query: 126 FPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLASNFLYSANETIRAQD 185
            P  LSV+CGL  GA  G++NGTLVARMKLPPFIVTLGMWQIVLA+NFLYSANETIR+QD
Sbjct: 122 IPAPLSVLCGLAAGAGIGFVNGTLVARMKLPPFIVTLGMWQIVLAANFLYSANETIRSQD 181

Query: 186 ISANASILQFFGQNFRI-------GNAVFTYGVVVMVLLVCLLWYVLNRTAWGRYVYAVG 238
           ISA A ILQFFG  FR+       G AVFTYG V+++LLV ++ YVL +TAWGR+VYAVG
Sbjct: 182 ISAQAPILQFFGNTFRLGADEAGRGGAVFTYGAVLLILLVLVIAYVLRQTAWGRHVYAVG 241

Query: 239 DDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANIESITAVVI 298
           DDP+AA+LAGV    +L+++YTLSGLICALAGW +IGR+GSVSPTAGQFANIESITAVVI
Sbjct: 242 DDPDAAELAGVQTRNVLVTVYTLSGLICALAGWVMIGRLGSVSPTAGQFANIESITAVVI 301

Query: 299 GGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVAIDQWIRKV 358
           GGISLFGGRGS++GMLFGALIVGVFSLGL+LMGTDPQWTYLLIG+LII AVA+DQWIRK 
Sbjct: 302 GGISLFGGRGSVLGMLFGALIVGVFSLGLKLMGTDPQWTYLLIGMLIIAAVAVDQWIRKA 361

Query: 359 AA 360
           AA
Sbjct: 362 AA 363


Lambda     K      H
   0.327    0.141    0.420 

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: 561
Number of extensions: 27
Number of successful extensions: 2
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: 360
Length of database: 363
Length adjustment: 29
Effective length of query: 331
Effective length of database: 334
Effective search space:   110554
Effective search space used:   110554
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 (21.7 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