GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Alicycliphilus denitrificans K601

Align ABC transporter (characterized, see rationale)
to candidate WP_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein

Query= uniprot:A0A166QFW2
         (381 letters)



>NCBI__GCF_000204645.1:WP_013723230.1
          Length = 377

 Score =  235 bits (599), Expect = 2e-66
 Identities = 140/349 (40%), Positives = 207/349 (59%), Gaps = 24/349 (6%)

Query: 4   LKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLID 63
           L++  ++K       LRD+ L +  GE + F+GPSGCGK+TLLR+IAGL++   G ++  
Sbjct: 20  LEIKGIHKNFENFSALRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIVQS 79

Query: 64  GRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQL 123
           GR ++ L   ER  G+VFQSYAL+P++++ +N+++GL   K  K  ++ RV +   +  L
Sbjct: 80  GRDISWLPASERDYGIVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAELLAMAGL 139

Query: 124 DKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRL 183
                + P +LSGGQ+QRVA+ RA+A  P +LL DEPLS LDA++RV++R EI RL  ++
Sbjct: 140 PTAGGKYPSQLSGGQQQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQKQV 199

Query: 184 GSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLS 243
           G T I VTHDQ EA++++D+IVV+N G +EQVG+P E+YERPAS FVA F+G  ++N L 
Sbjct: 200 GITTIMVTHDQEEALSMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFVG--KVNVLR 257

Query: 244 ARLQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPE-HVSLKAADGT---AGVV 299
            +    G+   V  +            +   G  +SL +RPE  V+     GT    GV+
Sbjct: 258 GQ-ALGGKRFRVGKME---IECEASEGSFRLGEDVSLYLRPEDRVAEHLEAGTPYRLGVL 313

Query: 300 VTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLH 348
           V  VE+LG               +C  EVSA    G  + L   L+ +H
Sbjct: 314 VNKVEFLGG--------------LCIAEVSAEALGGQSLGLHFSLNQMH 348


Lambda     K      H
   0.320    0.137    0.394 

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: 317
Number of extensions: 10
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: 381
Length of database: 377
Length adjustment: 30
Effective length of query: 351
Effective length of database: 347
Effective search space:   121797
Effective search space used:   121797
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: 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