GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Galbibacter marinus ck-I2-15

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_008991496.1 I215_RS08190 SIS domain-containing protein

Query= SwissProt::A0KYQ7
         (386 letters)



>NCBI__GCF_000300875.1:WP_008991496.1
          Length = 380

 Score =  273 bits (698), Expect = 6e-78
 Identities = 160/379 (42%), Positives = 235/379 (62%), Gaps = 23/379 (6%)

Query: 21  EQLTQYGAFWTAKEISQQPKMWRKV-SEQHSDNRTIAAWLTPILAKPQLRIILTGAGTSA 79
           + +T Y    T KEI  QP++W +  S      + IA +L+PIL    LRIILTGAG+SA
Sbjct: 3   KDITTYINKHTEKEIKAQPRLWNETFSLLVETKKDIALFLSPILQLKDLRIILTGAGSSA 62

Query: 80  YIGDVLAAHIQQHLPLATQQVEAISTTDIVSHPELYLRGNIPTLLISYGRSGNSPESMAA 139
           ++G+V    IQQ   L TQ V   +TTD+V+HPE +     PTLLIS+ RSGNSPES+ A
Sbjct: 63  FVGEVAQGTIQQQTNLPTQLV---ATTDLVTHPEAFFIKQRPTLLISFARSGNSPESLEA 119

Query: 140 VELAEQLVDDCYHLAITCNGQGKLANYCADKSHCYLYKLPDETHDVSFAMTSSFTCMYLA 199
             L +Q  D+ YHL ITCN +GKLAN+   K+  Y  +LP+ET+D S AMTSSFT M L 
Sbjct: 120 ASLLDQHCDNAYHLIITCNPEGKLANFDT-KNPLYSIQLPEETNDKSLAMTSSFTAMLLT 178

Query: 200 TLLIF-----APNSQALMQCIEMAEHILTERLADIRLQSEQPS-KRVVFLGGGPLKAIAQ 253
            LL+F         QA+   I + E +L  +  D+  +  + + +RVVFLG GP+  IA+
Sbjct: 179 ALLVFDIDNIESKQQAVTNMIAIGEDLL--KAEDVFKEIAKSNFERVVFLGSGPMVGIAR 236

Query: 254 EAALKYLELTAGQVVSAFESPLGFRHGPKSLVDSHTQVLVMMSSDPYTRQYDNDLIQELK 313
           E  LK  ELT GQV+   +S LGFRHGP+++V+++T V+ + S+DP+  +Y+ DL +++ 
Sbjct: 237 ECHLKLQELTDGQVICKHDSFLGFRHGPRAVVNANTLVVYLFSNDPHVFRYEKDLAEDIA 296

Query: 314 RDNQALSVLTLSEE----------LLTGSSGLNEVWLGLPFILWCQILAIYKAIQLKVSP 363
           RD + +  LT+++E          ++T +   ++    +P  L  Q+L ++K++ L + P
Sbjct: 297 RDARKIQSLTITDEPTLELENSKHIVTSAFKHSDNLNAVPTTLVGQLLGLHKSLTLGLDP 356

Query: 364 DNPCPTGQVNRVVQGVNVY 382
           DNP  +G +NRVVQGV +Y
Sbjct: 357 DNPSVSGAINRVVQGVTIY 375


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: 336
Number of extensions: 16
Number of successful extensions: 6
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: 380
Length adjustment: 30
Effective length of query: 356
Effective length of database: 350
Effective search space:   124600
Effective search space used:   124600
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