GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Sphingopyxis indica DS15

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_089214888.1 CHB69_RS04915 SIS domain-containing protein

Query= reanno::Caulo:CCNA_00453
         (363 letters)



>NCBI__GCF_900188185.1:WP_089214888.1
          Length = 348

 Score =  324 bits (831), Expect = 2e-93
 Identities = 178/340 (52%), Positives = 226/340 (66%), Gaps = 4/340 (1%)

Query: 27  THMFREAGEAARVAAVQLTANAPKIQALAQRLRANPPRVVVTCARGSSDHAATFARYLIE 86
           T MF EA  A      Q       I  + + L A+PP +VVTCARGSSDHAATFA+Y  E
Sbjct: 10  TLMFLEAASAGDAVERQFGCAQGVIIDILRSLAADPPSMVVTCARGSSDHAATFAKYAFE 69

Query: 87  TKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKSPDLLAAVKAAKAAGAHAVALVN 146
            + G +T+SA PS+SS+Y A   L G+L+LAISQSGKSPDLL AV+ A   GA  +ALVN
Sbjct: 70  RQLGWVTASAAPSISSIYQAPLKLGGSLFLAISQSGKSPDLLEAVERASHQGARTLALVN 129

Query: 147 VVDSPLAALADEVIPLHAGPELSVAATKSYIAALVAVTQLIAAW-TEDAELTAALQDLPT 205
             D+PL+ +AD  +PL AGPE SVAATKSYIA+L A+ +++ +    D  +   L  LP 
Sbjct: 130 APDTPLSKIADWTLPLCAGPENSVAATKSYIASLAAIARIVGSLERNDGGIAPDLAALPG 189

Query: 206 ALAAAWTLDWSLAVERLKTASNLYVLGRGVGFGVALEAALKFKETCGLHAEAFSAAEVLH 265
            L AAW LDWS        +  L+VLGRG G  +A EAALKFKETCG+HAEAFS AEV H
Sbjct: 190 LLRAAWRLDWSPMAAAFNESQGLFVLGRGPGLAIAQEAALKFKETCGIHAEAFSTAEVRH 249

Query: 266 GPMALVKDGFPALVFAQNDESRASVDEMAAGLRARGASVLIAGGG--GDAPDALPTLASH 323
           GPMAL   G P L+F Q+DES + VD +   L A GA +L+AG G  G A + LP + + 
Sbjct: 250 GPMALAATGLPMLIFRQDDESASGVDALIKELLAIGAKLLVAGSGPCGGAIN-LPVVDAP 308

Query: 324 PVLEPILMIQSFYRMANALSVARGYDPDSPPHLNKVTETI 363
             L+P+L IQSFY+  ++L+++RG+DPD PP L KVTET+
Sbjct: 309 AALQPMLQIQSFYKAISSLAISRGHDPDRPPLLRKVTETV 348


Lambda     K      H
   0.315    0.128    0.360 

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: 398
Number of extensions: 9
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: 363
Length of database: 348
Length adjustment: 29
Effective length of query: 334
Effective length of database: 319
Effective search space:   106546
Effective search space used:   106546
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 (21.6 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