GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Duganella sacchari Sac-22

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_072787251.1 BUA36_RS20885 SIS domain-containing protein

Query= reanno::pseudo3_N2E3:AO353_04455
         (336 letters)



>NCBI__GCF_900143065.1:WP_072787251.1
          Length = 337

 Score =  366 bits (940), Expect = e-106
 Identities = 195/336 (58%), Positives = 242/336 (72%)

Query: 1   MLEEALSSYKAVDAQLQQLDPLMIEIAGRLNRQPPQVAMTVARGSSDHAASYFAYLTMQH 60
           ML+EALS+   V  QL        E+  +L       A+T+ARGSSDHA +Y AYL M  
Sbjct: 2   MLKEALSAADCVAQQLANDGERYAELGRKLRSTSFSTALTIARGSSDHACAYVAYLIMAR 61

Query: 61  VGIPVASLPMSVVTMQQAPLKVSGQAVFAFSQSGQSPDLVNSLRLLRKRGALSISMVNAE 120
           +G  VASLPMS+VT+ ++PL        + SQSGQSPD+V  +R  R  GA +I++VN  
Sbjct: 62  LGRVVASLPMSLVTLNKSPLITRDTLAISISQSGQSPDVVEPIRYFRDGGATTIALVNDI 121

Query: 121 NSPLEAACEFSLPLCAGTESSVAATKSFIATLSASARLIAYWKQDPELLQAGLALPEGLR 180
           +SPL  A E+++PL AG E SVAATKSFI +L A ARL+A W+ DPELL    ALPE LR
Sbjct: 122 DSPLAQAAEWAMPLRAGKEQSVAATKSFITSLVAGARLVAAWQNDPELLAGLEALPESLR 181

Query: 181 DAATQDWSLAVDVLRDCQRLMVIGRGAGFAIAQEAALKLKETSAIQAEAFSSAEVKHGPM 240
            A T+DWS AV+VL   + +MV+GRG  F +A EA+LK KETSA+QAEAFS AE+KHGPM
Sbjct: 182 AATTEDWSKAVEVLTPARNIMVVGRGISFPVALEASLKFKETSALQAEAFSGAEIKHGPM 241

Query: 241 ALIDDNYPLLVFAPRGAEQAGLLSLAAEMRQRGARVLLAAPDDVSERDLTLSRAEHPALD 300
           ALI++ YPL++FA RG  QA LL LA EMR RGARVLLAAP DV++RDLTL  A  P LD
Sbjct: 242 ALIEEGYPLVIFATRGPTQASLLQLATEMRGRGARVLLAAPADVADRDLTLPVAATPDLD 301

Query: 301 PILAIQSFYVMAAGLAVARGMDPDQPRHLSKVTRTH 336
           PI+A+Q+FY MAA L+ ARG+DPDQPRHLSKVT+T+
Sbjct: 302 PIVAVQAFYKMAAELSAARGLDPDQPRHLSKVTKTN 337


Lambda     K      H
   0.318    0.130    0.362 

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: 7
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: 336
Length of database: 337
Length adjustment: 28
Effective length of query: 308
Effective length of database: 309
Effective search space:    95172
Effective search space used:    95172
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. 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