GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Methanococcus aeolicus Nankai-3

Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate WP_011973701.1 MAEO_RS04980 ABC transporter ATP-binding protein

Query= TCDB::P96483
         (377 letters)



>NCBI__GCF_000017185.1:WP_011973701.1
          Length = 258

 Score =  137 bits (344), Expect = 4e-37
 Identities = 75/209 (35%), Positives = 117/209 (55%), Gaps = 10/209 (4%)

Query: 20  AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDI 79
           AV+ ++ ++   EFL +VGPSGCGKST LRM+AGLE    G + +   +   +   D + 
Sbjct: 23  AVEDVNFSVNSNEFLSIVGPSGCGKSTLLRMIAGLEKPTSGTLIL---EGNKIEKPDAER 79

Query: 80  AMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGG 139
            MVFQ Y L P  TV  N+   L+I G+ K E  +  +   K++ L ++ +  P  LSGG
Sbjct: 80  GMVFQQYTLLPWKTVLGNVALGLEIKGMKKEERNKIAKNFIKLIGLEEFENSYPYELSGG 139

Query: 140 QRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEA 199
            +QRVA+ R +  +P++ LMDEP   LD + RV  + ++  +  +   T V++TH   EA
Sbjct: 140 MQQRVAIARTLANDPKIVLMDEPFGALDTQTRVILQNELLKIWEKDKKTVVFITHSVEEA 199

Query: 200 MTMGDRVAV-------LKDGLLQQVDSPR 221
           + + DRV +       +KD +   +D PR
Sbjct: 200 VYLSDRVIIMSARPGKIKDIVNIDIDRPR 228


Lambda     K      H
   0.317    0.135    0.379 

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: 208
Number of extensions: 7
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: 377
Length of database: 258
Length adjustment: 27
Effective length of query: 350
Effective length of database: 231
Effective search space:    80850
Effective search space used:    80850
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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