GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacC in Mariniradius saccharolyticus AK6

Align periplasmic glucoside 3-dehydrogenase (lacC subunit) (EC 1.1.99.13) (characterized)
to candidate WP_008625432.1 C943_RS06180 gluconate 2-dehydrogenase subunit 3 family protein

Query= reanno::Cola:Echvi_1848
         (183 letters)



>NCBI__GCF_000330725.2:WP_008625432.1
          Length = 185

 Score =  253 bits (646), Expect = 1e-72
 Identities = 127/185 (68%), Positives = 146/185 (78%), Gaps = 2/185 (1%)

Query: 1   MAMNRRDALKSFALMMGGTMVGANALLTGCTPDKQIEGLDFSPEEIDFLDEIGDTIIPTT 60
           MA+NRRDA+KSF +MMGG MVGANA+LTGC P+ QI GL+FSP++I FLDEIG+ IIPTT
Sbjct: 1   MAINRRDAIKSFVIMMGGAMVGANAILTGCKPEHQIIGLEFSPDDIAFLDEIGEAIIPTT 60

Query: 61  DTPGAKAVGIGSFMVMMVKDTYWEEEQKQFIDGLNSLRKGFKEEVGKDFMDASQEERTAY 120
           DTPGAKA  IG FMVMMVKDTY  E+Q+ F DGLN + K FK   GKDFM+A+ EERT+Y
Sbjct: 61  DTPGAKATKIGEFMVMMVKDTYAAEQQQAFTDGLNFIIKDFKASQGKDFMEATVEERTSY 120

Query: 121 LNKLNAAAREENGPK--YFNMLKDLTVLGYFTSEIGATQALNYVEVPGKWEPCIDYKKGD 178
           LN L A A    G       ML+DLTVLGYFTSEIGATQ L Y EVPG++EPCIDYK GD
Sbjct: 121 LNGLKAKAENPEGKNAAVVKMLQDLTVLGYFTSEIGATQQLRYYEVPGRYEPCIDYKPGD 180

Query: 179 KAHAI 183
           KA+AI
Sbjct: 181 KAYAI 185


Lambda     K      H
   0.316    0.135    0.395 

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: 172
Number of extensions: 7
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: 183
Length of database: 185
Length adjustment: 19
Effective length of query: 164
Effective length of database: 166
Effective search space:    27224
Effective search space used:    27224
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: 44 (21.6 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