GapMind for catabolism of small carbon sources

 

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

Align D-galactosamine-6-phosphate deaminase AgaS; GalN-6-P deaminase; Glucosamine-6-phosphate deaminase; GlcN-6-P deaminase; EC 3.5.99.-; EC 3.5.99.6 (characterized)
to candidate WP_072786695.1 BUA36_RS18070 SIS domain-containing protein

Query= SwissProt::A0KYQ7
         (386 letters)



>NCBI__GCF_900143065.1:WP_072786695.1
          Length = 378

 Score =  278 bits (711), Expect = 2e-79
 Identities = 158/361 (43%), Positives = 224/361 (62%), Gaps = 8/361 (2%)

Query: 27  GAFWTAKEISQQPKMWRKVSEQ-HSDNRTIAAWLTPILAKPQLRIILTGAGTSAYIGDVL 85
           G   TA+EI+ QP +WR+++    ++   IAA+L   L  PQ R+ILTGAG+SAY+G+++
Sbjct: 16  GGLETAEEIAHQPALWRELAAHLGAEQSRIAAFLGDSLRNPQQRVILTGAGSSAYVGEII 75

Query: 86  AAHIQQHLPLATQQVEAISTTDIVSHPELYLRGNIPTLLISYGRSGNSPESMAAVELAEQ 145
           A  I    P    QV AISTT +++HP LYL  + PTLL+S+ RSGNSPES  AV+L   
Sbjct: 76  ADEINAAWPC---QVRAISTTSLLTHPALYLDSSAPTLLVSFARSGNSPESTGAVQLVRD 132

Query: 146 LVDDCYHLAITCNGQGKLANYCADKSHCYLYKLPDETHDVSFAMTSSFTCMYLATLLIFA 205
           LV +   L ITCN +G LA   A+ S      +P  + D  FAMTSSFTCM LA L    
Sbjct: 133 LVPNARFLNITCNAEGDLAQQGANDSASLNLMMPAASCDRGFAMTSSFTCMLLAALSALD 192

Query: 206 PNSQ--ALMQCIEMAEHILTERLADIRLQSEQPSKRVVFLGGGPLKAIAQEAALKYLELT 263
           P+ Q   L +  ++ E       A +   + +   RV++LG GPL+A+A+EAALK +ELT
Sbjct: 193 PDFQPERLNKLAQLGEQAQGLWSAPVAALAARRVSRVIYLGSGPLEALAKEAALKIMELT 252

Query: 264 AGQVVSAFESPLGFRHGPKSLVDSHTQVLVMMSSDPYTRQYDNDLIQELKRDNQALSVLT 323
           AG V++   S LGFRHGPK+ V+  T VL+  S+DP +R+Y++DL++EL+RD  A  VLT
Sbjct: 253 AGSVMTMANSALGFRHGPKAAVNPETLVLLFRSADPLSRRYEHDLVEELRRDQVAADVLT 312

Query: 324 LSE--ELLTGSSGLNEVWLGLPFILWCQILAIYKAIQLKVSPDNPCPTGQVNRVVQGVNV 381
           +    +    +    + WL   ++L  Q  A++++  L++ PDNP   G VNRVVQGV +
Sbjct: 313 VGAGGDFSIDTPAWPDAWLAPLWLLMAQQYALHQSALLQLRPDNPFKGGIVNRVVQGVTI 372

Query: 382 Y 382
           Y
Sbjct: 373 Y 373


Lambda     K      H
   0.319    0.133    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: 358
Number of extensions: 15
Number of successful extensions: 5
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: 386
Length of database: 378
Length adjustment: 30
Effective length of query: 356
Effective length of database: 348
Effective search space:   123888
Effective search space used:   123888
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: 50 (23.9 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