GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolC in Halococcus hamelinensis 100A6

Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92) (characterized)
to candidate WP_049904537.1 C447_RS14190 sugar kinase

Query= reanno::Phaeo:GFF709
         (330 letters)



>NCBI__GCF_000336675.1:WP_049904537.1
          Length = 318

 Score = 97.8 bits (242), Expect = 3e-25
 Identities = 85/288 (29%), Positives = 125/288 (43%), Gaps = 7/288 (2%)

Query: 38  AQDMMVAMGGSSANIAAGLVKMGCRSALVTSVSDDAVGWYCLNQLDHYGVDRTHVKRITG 97
           A +   ++ G+  N+A GL ++G      + +  D  G Y    +   GVD T V+  T 
Sbjct: 26  AHEFEKSLAGAETNVAIGLARLGHDVGWYSKLGTDPHGEYLEFFVRGEGVDTTTVE-FTD 84

Query: 98  EYRTSLAVYESRVEDHQSVIYRNNAADFQMTIADVEAVDY---SQYSALITAGTVFAAEP 154
           E  T +   E R     +V Y  + +   +   D   VDY   ++Y  L T  T   +E 
Sbjct: 85  EAPTGIMFKERREFGEPAVHYYRHGSAASLMSPDDLPVDYLTNAEYLHL-TGITPALSES 143

Query: 155 SRSATFRAFDLARAAGLPIIFDVDYRPYSWPSPEVAADVLSRAGAMSDIIVGNDEEFGFM 214
            R AT  A + A  AG+ + FD + R   W S E   + +    ++SDI++   EE G  
Sbjct: 144 CRDATLLAAERATEAGMTVSFDPNVRRKLWESDERMRETMLDLVSLSDIVLPGIEE-GAA 202

Query: 215 AGGIDKGRAKARALAETSASVVVYKMGPKGAVTFADGQEIRTGIYPVD-ALKPTGAGDSF 273
             G D   A A A  +  A   V K+G  GAV        R   Y V+  + P GAGD F
Sbjct: 203 LFGTDDPEAIAAACLDHGAGTAVVKLGAAGAVVADGSTTERVSGYDVERVVDPVGAGDGF 262

Query: 274 MAGFLASLSEGRPMKDAILRGSACASVVVAKPGCAPAMPDLAALEAFL 321
            AGFLAS  EG+   +A    +A  +      G    +P    L+ F+
Sbjct: 263 AAGFLASRIEGQGPVEATETANAVGAFATTVAGDTEGLPTRKELDVFV 310


Lambda     K      H
   0.319    0.132    0.386 

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: 237
Number of extensions: 17
Number of successful extensions: 4
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: 330
Length of database: 318
Length adjustment: 28
Effective length of query: 302
Effective length of database: 290
Effective search space:    87580
Effective search space used:    87580
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: 48 (23.1 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