GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Alicycliphilus denitrificans K601

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_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein

Query= TCDB::P96483
         (377 letters)



>NCBI__GCF_000204645.1:WP_013723230.1
          Length = 377

 Score =  219 bits (559), Expect = 7e-62
 Identities = 136/355 (38%), Positives = 206/355 (58%), Gaps = 21/355 (5%)

Query: 20  AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDI 79
           A+  +D+ +  GE L  +GPSGCGK+T LR++AGLE    G+I    RD++ LP  +RD 
Sbjct: 34  ALRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIVQSGRDISWLPASERDY 93

Query: 80  AMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGG 139
            +VFQ+YAL+P++T+A+N+ + L    + KAEI+ +V E   +  L     + P  LSGG
Sbjct: 94  GIVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAELLAMAGLPTAGGKYPSQLSGG 153

Query: 140 QRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEA 199
           Q+QRVA+ RA+   P + L+DEPLS LDA +RV  R +I  LQ+++GITT+ VTHDQ EA
Sbjct: 154 QQQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQKQVGITTIMVTHDQEEA 213

Query: 200 MTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFGNSV 259
           ++M DR+ V+  G+++QV +P  +Y++PA+ FVA F+G   +N++      GG +F    
Sbjct: 214 LSMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFVGK--VNVLRGQAL-GGKRFRVGK 270

Query: 260 VPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVNVVEE 319
           + +  EA   + +    V++ +RPE          VA  L    A  P  L V VN VE 
Sbjct: 271 MEIECEASEGSFRLGEDVSLYLRPE--------DRVAEHL---EAGTPYRLGVLVNKVEF 319

Query: 320 LGADGYVYGTAE-VGGEVKDLVVRVNGRQVPE----KGSTLHVVPRPGETHVFST 369
           LG       +AE +GG+   L   +N  Q+ +    +G  + +  R     VFST
Sbjct: 320 LGGLCIAEVSAEALGGQSLGLHFSLN--QMHDLGICEGRRIDIALRASRIRVFST 372


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: 339
Number of extensions: 14
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: 377
Length of database: 377
Length adjustment: 30
Effective length of query: 347
Effective length of database: 347
Effective search space:   120409
Effective search space used:   120409
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: 50 (23.9 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