GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Alicycliphilus denitrificans K601

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate WP_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_000204645.1:WP_013723230.1
          Length = 377

 Score =  207 bits (528), Expect = 3e-58
 Identities = 116/296 (39%), Positives = 183/296 (61%), Gaps = 19/296 (6%)

Query: 4   LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63
           L++  I+K + N    ++ + +L +   E + F+GPSGCGK+T LR+IAGLE  T G++ 
Sbjct: 20  LEIKGIHKNFENFS--ALRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIV 77

Query: 64  IDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEIL 123
              + ++     +RD  +VFQ+YAL+P++++ EN+A+GL   K +K +I  RV E   + 
Sbjct: 78  QSGRDISWLPASERDYGIVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAELLAMA 137

Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHR 183
           GL     + P+ LSGGQ+QRVA+ RA+  +  + L+DEPLS LDA +RV +RAEI ++ +
Sbjct: 138 GLPTAGGKYPSQLSGGQQQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQK 197

Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVA 243
           ++G TTI VTHDQ EA++++DRIV+M+           G IEQ+GTP E+Y  PA+ FVA
Sbjct: 198 QVGITTIMVTHDQEEALSMSDRIVVMNH----------GVIEQVGTPMEIYERPASPFVA 247

Query: 244 GFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPED 299
            F+G       +V V + + +      +   + + +  E    LG+ V+L +RPED
Sbjct: 248 NFVG-------KVNVLRGQALGGKRFRVGKMEIECEASEGSFRLGEDVSLYLRPED 296


Lambda     K      H
   0.318    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: 337
Number of extensions: 17
Number of successful extensions: 3
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 (21.7 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