GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Alkalihalobacterium alkalinitrilicum DSM 22532

Align glucokinase; EC 2.7.1.2 (characterized)
to candidate WP_075388699.1 BK574_RS12335 ROK family glucokinase

Query= CharProtDB::CH_014478
         (324 letters)



>NCBI__GCF_002019605.1:WP_075388699.1
          Length = 316

 Score =  393 bits (1009), Expect = e-114
 Identities = 196/319 (61%), Positives = 241/319 (75%), Gaps = 6/319 (1%)

Query: 3   MDDKWLVGVDLGGTTIKMAFINHYGEIIHKWEINTDVSEQGRKIPTDIAKAIDKKLNDLG 62
           M  KW VGVDLGGTTIK+AF++ YG+II K E+ T+ +  G  I TDIAK ID+ L  LG
Sbjct: 1   MVTKWFVGVDLGGTTIKLAFVDPYGDIIFKGEVPTNTTNGGTNITTDIAKWIDQALEHLG 60

Query: 63  EVKSRLVGIGIGAPGPVNFANGSIEVAVNLGWEKFPIKDILEVETSLPVVVDNDANIAAI 122
             K RL  IG+GAPG +N   G I  AVN+GW+ F +KD LE++TSLPV +DNDANIAA+
Sbjct: 61  VSKDRLHSIGMGAPGFINMETGYIYQAVNIGWKDFHLKDRLEMDTSLPVTIDNDANIAAL 120

Query: 123 GEMWKGAGDGAKDLLCVTLGTGVGGGVIANGEIVQGVNGAAGEIGHITSIPEGGAPCNCG 182
           GEMW+GAG+GAK+LLCVTLGTGVGGGVI NG IV GVNG AGEIGHIT+IP+GG PCNCG
Sbjct: 121 GEMWRGAGNGAKNLLCVTLGTGVGGGVIVNGSIVHGVNGMAGEIGHITAIPKGGFPCNCG 180

Query: 183 KTGCLETIASATGIVRLTMEELTETDKPSELRTVLEQNGQVTSKDVFDAARSKDGLAMHV 242
           K GCLETI+SATGI R+  E +  +D P+ L      NG + +K VF+AA   D  A+ V
Sbjct: 181 KAGCLETISSATGISRIAKEFV--SDFPNSLLA----NGNINAKMVFEAAEKNDECALKV 234

Query: 243 VDKVAFHLGLALANSANALNPEKIVLGGGVSRAGEVLLAPVRDYFKRFAFPRVAQGAELA 302
           +D + ++LG ALAN AN+LNPEKIV+GGGVS+AGE LL P+ ++F+ F  PRVAQ   + 
Sbjct: 235 IDHITYYLGFALANLANSLNPEKIVIGGGVSKAGETLLKPLENHFQLFVLPRVAQSVSIV 294

Query: 303 IATLGNDAGIIGGAWLVKS 321
            ATLGNDAG+IGGAWL K+
Sbjct: 295 PATLGNDAGVIGGAWLAKT 313


Lambda     K      H
   0.316    0.137    0.404 

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: 373
Number of extensions: 11
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: 324
Length of database: 316
Length adjustment: 28
Effective length of query: 296
Effective length of database: 288
Effective search space:    85248
Effective search space used:    85248
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: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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