GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Amantichitinum ursilacus IGB-41

Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate WP_053938863.1 WG78_RS16125 amino acid ABC transporter ATP-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_2050
         (263 letters)



>NCBI__GCF_001294205.1:WP_053938863.1
          Length = 246

 Score =  235 bits (599), Expect = 8e-67
 Identities = 123/242 (50%), Positives = 162/242 (66%), Gaps = 11/242 (4%)

Query: 19  LRKQYG-PLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIMLDGESI 77
           + K YG    VLK + L +++G VV + G SGSGK+TL+R +N LE    G+I       
Sbjct: 7   VNKWYGRDHHVLKNISLEVKQGEVVVVCGPSGSGKSTLIRTINQLEPVNDGEIW------ 60

Query: 78  GYDDIDGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLPKDEAVA 137
               +DG +V HP   I R R   G  FQ FNL+PHL+ LQN+TL  +KV+K+ + +A  
Sbjct: 61  ----VDGVQVNHPRTNINRLREEVGFVFQHFNLYPHLSVLQNITLAPVKVRKMSQADADQ 116

Query: 138 LAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPELVGEV 197
              + LERVGL  +RD +P QLSGGQQQRVAIAR +AM P +MLFDE TSALDPE++GEV
Sbjct: 117 RGMELLERVGLSNKRDAYPSQLSGGQQQRVAIARGLAMQPKVMLFDEPTSALDPEMIGEV 176

Query: 198 LNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSPRLAEF 257
           L V++ LAE GMTM++VTHEM FA EV+D++VF++ G I EQ  P + F  PQ  R  +F
Sbjct: 177 LKVMQNLAESGMTMMVVTHEMGFAREVADRVVFLDHGEILEQAAPAQFFNNPQCDRAQQF 236

Query: 258 LK 259
           L+
Sbjct: 237 LR 238


Lambda     K      H
   0.320    0.138    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: 189
Number of extensions: 10
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: 263
Length of database: 246
Length adjustment: 24
Effective length of query: 239
Effective length of database: 222
Effective search space:    53058
Effective search space used:    53058
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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