GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecE in Herbaspirillum seropedicae SmR1

Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate HSERO_RS21910 HSERO_RS21910 iron ABC transporter ATP-binding protein

Query= CharProtDB::CH_088321
         (255 letters)



>FitnessBrowser__HerbieS:HSERO_RS21910
          Length = 263

 Score =  139 bits (351), Expect = 5e-38
 Identities = 89/242 (36%), Positives = 125/242 (51%), Gaps = 4/242 (1%)

Query: 2   TLRTENLTVSYGTDKVLNDVSL-SLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVF 60
           +L    L V+YG   V+  + L  L  G +TAL+GPNG GKSTLL     L   Q+G+V 
Sbjct: 5   SLCVAGLKVAYGRHSVIQGLDLPELTAGSVTALLGPNGSGKSTLLRTLGGLTRAQAGSVR 64

Query: 61  LGDNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVN 120
           LG   +    +   A+ +  +PQ    P  ++V E V            R   ++  RV 
Sbjct: 65  LGPTELAQADAAARAQHVVYMPQSLPRPVHLSVFESVLVAAQALQRT--RPDTQELERVQ 122

Query: 121 VAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRL 180
             +    I HLA R L ELSGGQRQ A LA  L +   V+LLDEP + LD+N+Q  +M L
Sbjct: 123 ALLQHLGIGHLAQRHLDELSGGQRQLAALAQALVRRPRVLLLDEPLSALDLNYQYLVMDL 182

Query: 181 M-GELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEA 239
           +  E R  G   + VLHDLN A R+ D+ +++  G ++  G   EV+TP  L   + V+ 
Sbjct: 183 LRQETRLHGLVTLVVLHDLNTAFRHVDRALLLHQGRLLCAGAAREVITPATLAQAYGVDG 242

Query: 240 EI 241
            I
Sbjct: 243 RI 244


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: 185
Number of extensions: 5
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: 255
Length of database: 263
Length adjustment: 24
Effective length of query: 231
Effective length of database: 239
Effective search space:    55209
Effective search space used:    55209
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: 47 (22.7 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