GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Alicycliphilus denitrificans K601

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

Query= reanno::Smeli:SMc04256
         (361 letters)



>NCBI__GCF_000204645.1:WP_013723230.1
          Length = 377

 Score =  209 bits (533), Expect = 7e-59
 Identities = 124/302 (41%), Positives = 176/302 (58%), Gaps = 7/302 (2%)

Query: 3   SVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFI 62
           ++ ++ +  NF   + L  ++L +  GE L  LG SGCGK+TLL  IAGL   + G I  
Sbjct: 19  ALEIKGIHKNFENFSALRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIVQ 78

Query: 63  KDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQ 122
             R+++W    +R  G+VFQSYAL+P +T+ +N+++GL   K+  AEI+ RV     +  
Sbjct: 79  SGRDISWLPASERDYGIVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAELLAMAG 138

Query: 123 IQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQS 182
           +     + PS+LSGGQ+QRVA+ RAL  +  + L DEPLS LDA +R  LR EI+RL + 
Sbjct: 139 LPTAGGKYPSQLSGGQQQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQKQ 198

Query: 183 LKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFF 242
           +  T I VTHDQ EAL+++DRI VM  GVI+Q+  PM IY  P + FVA F+G   +N  
Sbjct: 199 VGITTIMVTHDQEEALSMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFVG--KVNVL 256

Query: 243 RGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTHQA 302
           RG+     G+ F R G +  +  A     RL  G+ V L LRPE    +    G P    
Sbjct: 257 RGQA--LGGKRF-RVGKMEIECEASEGSFRL--GEDVSLYLRPEDRVAEHLEAGTPYRLG 311

Query: 303 VV 304
           V+
Sbjct: 312 VL 313


Lambda     K      H
   0.320    0.137    0.392 

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: 328
Number of extensions: 15
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: 361
Length of database: 377
Length adjustment: 30
Effective length of query: 331
Effective length of database: 347
Effective search space:   114857
Effective search space used:   114857
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