GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecE in Methanobacterium arcticum M2

Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate WP_048081429.1 EI99_RS07905 ABC transporter ATP-binding protein

Query= CharProtDB::CH_088321
         (255 letters)



>NCBI__GCF_000746075.1:WP_048081429.1
          Length = 260

 Score =  152 bits (384), Expect = 7e-42
 Identities = 78/227 (34%), Positives = 130/227 (57%)

Query: 15  DKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLGDNPINMLSSRQL 74
           + + NDV+LSL  G +  ++GPNG GKSTL+ C + LL   SG + + +  I+ L+   L
Sbjct: 18  EDIFNDVNLSLENGDVLCILGPNGTGKSTLIKCMNGLLKLNSGNILINNQSIHSLNKNDL 77

Query: 75  ARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVAMNQTRINHLAVR 134
           A+ +  +PQ H +    +V ++V  GR P LSL      +D      A+    I+HL  +
Sbjct: 78  AKIIGYIPQSHNSTFAFSVFDVVLMGRAPHLSLTSVPGEKDCKIAEEALKSLGISHLTDK 137

Query: 135 RLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLMGELRTQGKTVVAV 194
             TE+SGG+RQ   +A VLAQ   ++LLDEPT++LD  +Q+  + ++ +L   G +V+  
Sbjct: 138 TYTEISGGERQMVLIARVLAQQPQILLLDEPTSHLDFGNQIRTLDVINKLAENGLSVIMT 197

Query: 195 LHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAEI 241
            H  + A    +++ +M  G +M  GTPE V+T   +R  ++++ +I
Sbjct: 198 SHFPDHAFLSSNKVAIMNGGTIMEMGTPESVITEENMRRAYNIDVKI 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: 163
Number of extensions: 4
Number of successful extensions: 1
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: 260
Length adjustment: 24
Effective length of query: 231
Effective length of database: 236
Effective search space:    54516
Effective search space used:    54516
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 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