GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecC in Cupriavidus basilensis 4G11

Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate RR42_RS16135 RR42_RS16135 ABC transporter permease

Query= SwissProt::P15030
         (332 letters)



>FitnessBrowser__Cup4G11:RR42_RS16135
          Length = 335

 Score =  179 bits (453), Expect = 1e-49
 Identities = 121/342 (35%), Positives = 185/342 (54%), Gaps = 20/342 (5%)

Query: 1   MTAIKHPVLLWGLPVAALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLR 60
           M  ++  + +W +  AA + +F LSL    ++P+SGA    AL  G   T   A+V+ LR
Sbjct: 1   MPDMRRALAIWLMLAAAGVAVFLLSL-AVGSVPLSGAQVWHALCGGADDTAG-AIVRELR 58

Query: 61  LPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYS 120
           LPR+  A   G  LAL G L+Q L  NP+A P +LG++ GAA   ALT+ L   P+  ++
Sbjct: 59  LPRAAAAFACGGLLALTGALMQVLLRNPLAEPYVLGVSGGAATG-ALTAMLMMWPL--WT 115

Query: 121 LSFIAACGGGVSWLLVMTAG----------GGFRHTHDRNKLILAGIALSAFCMGLTRIT 170
           +   AA G   S +LV T            GG  H    ++L+L G+ L+A    L  + 
Sbjct: 116 VQAGAAGGALFSMVLVATLARRDLLHPQVQGG--HHEAGSRLLLTGVILAAGWGALITLI 173

Query: 171 LLLA-EDHAYGIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAH 229
           L +A E    G+ +WL G +       +   L  +  AV + + +A  LN + + ++ A 
Sbjct: 174 LSVAPEARLRGMLFWLTGDLGGTASYGL--ALGALALAVLLAMPMARSLNAMLMGETVAQ 231

Query: 230 TLGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLL 289
            LGV +  +RL + +L  L +   ++ AG + F+GL+VPHL R   G DQR +LP S LL
Sbjct: 232 ALGVRVGAVRLSVFVLASLAIAVAITSAGSIGFVGLVVPHLVRLAWGNDQRLMLPASALL 291

Query: 290 GATLMLLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRRR 331
           G TL++ AD++AR +  P  LP G + AL+G P F++L+ RR
Sbjct: 292 GGTLLMAADLVARTVIAPAQLPVGVITALLGVPTFLFLLLRR 333


Lambda     K      H
   0.327    0.140    0.436 

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: 320
Number of extensions: 16
Number of successful extensions: 3
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: 332
Length of database: 335
Length adjustment: 28
Effective length of query: 304
Effective length of database: 307
Effective search space:    93328
Effective search space used:    93328
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 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