GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Alicycliphilus denitrificans K601

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

Query= uniprot:A0A165KQ08
         (355 letters)



>NCBI__GCF_000204645.1:WP_013723230.1
          Length = 377

 Score =  244 bits (624), Expect = 2e-69
 Identities = 136/290 (46%), Positives = 187/290 (64%), Gaps = 10/290 (3%)

Query: 2   ASSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPT 61
           A +L+I GI+K F    ++   LR +D+ V  GE L  +GPSGCGK+TLL IIAGL+  T
Sbjct: 17  APALEIKGIHKNF----ENFSALRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQT 72

Query: 62  EGEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDE 121
            G I   G+++  +P  +RD  +VFQSYAL+P L++A+N+ + L   KM K E Q R+ E
Sbjct: 73  SGSIVQSGRDISWLPASERDYGIVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAE 132

Query: 122 VAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEI 181
           + AM  +     + PSQLSGGQ+QRVA+ RALA  P L L DEPLS LDA +RV +RAEI
Sbjct: 133 LLAMAGLPTAGGKYPSQLSGGQQQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEI 192

Query: 182 KRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGS 241
           +RL +  GIT++ VTHDQ EA+++  RI VM  GV++Q+GTP EIY RPA+ +VA F+G 
Sbjct: 193 RRLQKQVGITTIMVTHDQEEALSMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFVGK 252

Query: 242 PTMNLLRGAVTGG-QFGIQGAALNLAPPPSS---ANEVLLGVRPEHLVMQ 287
             +N+LRG   GG +F +    +       S     +V L +RPE  V +
Sbjct: 253 --VNVLRGQALGGKRFRVGKMEIECEASEGSFRLGEDVSLYLRPEDRVAE 300


Lambda     K      H
   0.318    0.135    0.388 

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: 311
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: 355
Length of database: 377
Length adjustment: 30
Effective length of query: 325
Effective length of database: 347
Effective search space:   112775
Effective search space used:   112775
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: 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