GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecE in Pseudomonas fluorescens FW300-N2E2

Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate Pf6N2E2_3544 ABC transporter (iron.B12.siderophore.hemin) , ATP-binding component

Query= CharProtDB::CH_088321
         (255 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3544
          Length = 262

 Score =  164 bits (414), Expect = 2e-45
 Identities = 92/233 (39%), Positives = 137/233 (58%), Gaps = 3/233 (1%)

Query: 18  LNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLGDNPINMLSSRQLARR 77
           L DV+L +  G+   LIGPNG GK++LL C  R   P  G V L  + +   SSR  A+R
Sbjct: 25  LRDVTLQVAAGEFVGLIGPNGSGKTSLLRCAYRFSRPAQGEVKLAHHNVWQQSSRWSAQR 84

Query: 78  LSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVAMNQTRINHLAVRRLT 137
           ++++ Q      G+TV+E+V+ GR P   L+   + +D   V  A+    +         
Sbjct: 85  IAVVLQEFPDAFGLTVEEVVAMGRTPHKGLFDGDNHDDRRLVLQALESAGLAGFGDHAFA 144

Query: 138 ELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLMGELRTQGKTVVAVLHD 197
            LSGG++QR  LA  LAQ   +++LDEPT +LD ++Q+ L++L+  L   G   +A LHD
Sbjct: 145 TLSGGEKQRVILARALAQQPQLLILDEPTNHLDPHYQLQLLQLIKGL---GIGTLASLHD 201

Query: 198 LNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAEIHPEPVSGRP 250
           LN A+ +CD+L V+ +G ++A GTP EV+T  LLR VF +EA +   P+SG P
Sbjct: 202 LNLAAAFCDRLYVIEHGRIVASGTPREVLTVELLREVFGIEALVDEHPLSGYP 254


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: 171
Number of extensions: 3
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: 262
Length adjustment: 24
Effective length of query: 231
Effective length of database: 238
Effective search space:    54978
Effective search space used:    54978
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