GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecE in Sphingomonas koreensis DSMZ 15582

Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate Ga0059261_0484 Ga0059261_0484 ABC-type multidrug transport system, ATPase component

Query= CharProtDB::CH_088321
         (255 letters)



>FitnessBrowser__Korea:Ga0059261_0484
          Length = 245

 Score =  105 bits (261), Expect = 1e-27
 Identities = 82/250 (32%), Positives = 127/250 (50%), Gaps = 21/250 (8%)

Query: 6   ENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFL-GDN 64
           ++++++YG  +VL  ++LS+P G ITAL+G NG GKST L      +  QSGT+ + G +
Sbjct: 11  QDVSLAYGAQEVLRGLTLSVPAGSITALLGGNGAGKSTTLAALLGFVRAQSGTILVCGVD 70

Query: 65  PINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNV--A 122
           P +     +  RR++ LP++    E ++  E   Y           LS E +AR ++  A
Sbjct: 71  PGSDPDGAR--RRIAYLPENVALYEHLSATENAEYLL--------ALSGEQHARRDITEA 120

Query: 123 MNQTRINHLAV-RRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLM 181
                +   A  +RL   S G RQ+  +A+ L +  PV+LLDEPT+ LD     D   L+
Sbjct: 121 FAAAGLQEEAWDQRLGGFSKGMRQKVAIAVALLRRVPVLLLDEPTSGLDPRATADFNALV 180

Query: 182 GELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAEI 241
            ++R +G  V+ V HDL  A+   D++  + NG V      +EV   G  R  F V A  
Sbjct: 181 AQVRDRGTAVLMVTHDLLSAADVADRIAFLENGRV-----TDEVAASGPER--FDVRALH 233

Query: 242 HPEPVSGRPM 251
               V G P+
Sbjct: 234 ARFQVGGEPL 243


Lambda     K      H
   0.320    0.134    0.393 

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: 143
Number of extensions: 5
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: 255
Length of database: 245
Length adjustment: 24
Effective length of query: 231
Effective length of database: 221
Effective search space:    51051
Effective search space used:    51051
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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