GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Alicycliphilus denitrificans K601

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate WP_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein

Query= reanno::Dino:3607124
         (338 letters)



>NCBI__GCF_000204645.1:WP_013723230.1
          Length = 377

 Score =  226 bits (577), Expect = 5e-64
 Identities = 141/344 (40%), Positives = 202/344 (58%), Gaps = 33/344 (9%)

Query: 4   IKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIG 63
           ++I  I+K +    AL DI+L +  GE + F+GPSGCGK+TLLR +AGLE  +SG I   
Sbjct: 20  LEIKGIHKNFENFSALRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIVQS 79

Query: 64  GRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKE----RIAEAAR 119
           GRD++ +  ++RD  +VFQSYAL+P++T+ EN+ +G+ VNG    +RK     R+AE   
Sbjct: 80  GRDISWLPASERDYGIVFQSYALFPNLTIAENVAYGL-VNG---KMRKAEIQARVAELLA 135

Query: 120 VLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGL 179
           +  L     + P QLSGGQ+QRVA+ RA+  NP + L DEPLS LDA +RV++R E+  L
Sbjct: 136 MAGLPTAGGKYPSQLSGGQQQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRL 195

Query: 180 HKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAM 239
            KQ+G T I VTHDQ EA++M+D+IVV+N G IEQVG+PM++Y +P S FVA F+G   +
Sbjct: 196 QKQVGITTIMVTHDQEEALSMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFVGK--V 253

Query: 240 NVFSSD--------VGLQDISLDASAAFVGCRPEHIEIVPDGDGHIAATVHVKERLGGES 291
           NV            VG  +I  +AS            +  D   ++     V E L   +
Sbjct: 254 NVLRGQALGGKRFRVGKMEIECEASEG-------SFRLGEDVSLYLRPEDRVAEHLEAGT 306

Query: 292 LLYLGLKG------GGQIVARVGGDDETKVGAAVSLRFSRHRLH 329
              LG+        GG  +A V    E   G ++ L FS +++H
Sbjct: 307 PYRLGVLVNKVEFLGGLCIAEVSA--EALGGQSLGLHFSLNQMH 348


Lambda     K      H
   0.320    0.139    0.396 

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: 352
Number of extensions: 16
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: 338
Length of database: 377
Length adjustment: 29
Effective length of query: 309
Effective length of database: 348
Effective search space:   107532
Effective search space used:   107532
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: 49 (23.5 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