GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Desulfotomaculum hydrothermale Lam5

Align hexokinase (EC 2.7.1.1) (characterized)
to candidate WP_008410212.1 DESHY_RS02610 hexokinase

Query= BRENDA::Q6X271
         (513 letters)



>NCBI__GCF_000315365.1:WP_008410212.1
          Length = 436

 Score =  224 bits (572), Expect = 4e-63
 Identities = 163/471 (34%), Positives = 244/471 (51%), Gaps = 50/471 (10%)

Query: 44  TSKTVQQAEKMSQEFRQSSSTPLPLLHQVADALVQEMYAGLASEGGSDQLKMLPTYVENL 103
           T   +Q+ E++   F  SS      + ++A  L  EM  GL  +G    L+MLPT+++ L
Sbjct: 2   TKLLIQKLEQIENAFYLSSVQ----VRELAKKLQTEM-TGLPGQGS---LQMLPTFMQ-L 52

Query: 104 PSGSEKGLFYAVDLGGTNFRVLRVELGGKTGQILSQEFKEVVIPPE------LMVGTGKD 157
           P+GSE G F AVD GGTN R+  VEL G+    + ++    +  P           TG+ 
Sbjct: 53  PAGSETGTFLAVDFGGTNVRLQLVELLGRGQYAIKKQHSFRLKDPSGRYDFTARETTGEA 112

Query: 158 LFDFIAGTLASFVDTEDESIKAHFVQSGKTRESGFAFSFPVRQTSVKSGIVIHWTKGFKV 217
           LFDF+AG +ASF++         F  S      G  FSFP RQ +    +++HWTK F+ 
Sbjct: 113 LFDFLAGQIASFME-------GTFATS-----LGLTFSFPCRQLAANKAVLLHWTKEFQT 160

Query: 218 DDAVGKDIVKQFQDAIS-RSNHQIMISALVNDTVGTLAGGRFNFDEETMIGCIIGTGTNA 276
              VG++I+     A++ R    +  +AL+NDT GTL    ++ +    IG I GTG N 
Sbjct: 161 SAVVGREIMGLLAGALADRGLAHLQPAALINDTTGTLLTAAYS-NPHADIGSICGTGHNT 219

Query: 277 CYVERADAVHKWDEPLPKSGEMVINMEWGNFRSPYLPRTFADETVDKDSVNPGDQWFEKM 336
           CY +             K   M+INME GNF+   L  T  D  +D +S  PG Q  EK 
Sbjct: 220 CYFKT------------KEPAMIINMEAGNFKQFAL--TAYDRLLDSNSRRPGTQLLEKA 265

Query: 337 ISGMYLGEIVRLVLARMAKEAELFGGNVPVKLLERLTLGTPHVSKIHLDNSPDLDVVAKV 396
           ++G YLGEI RL+L  M ++  LF G++P  + ++ T+ T  ++ +  DNSP L  + + 
Sbjct: 266 VAGRYLGEICRLILLDMVEQGLLFRGSIPALVRQQQTIDTSELALLAADNSPSLLHIDRW 325

Query: 397 LKDVFEIETTTLEERKIVHEVCDIMGERGGRLAAAGLYGILKKIGRTGKSRNGSKKKTVI 456
           L     I  TTL +R+++ ++   +  R  RL  A   GIL++I        G +++ VI
Sbjct: 326 LAARQNIHPTTLTDRQVLKKIALTVISRSARLVGATYIGILQQID------PGLQRRHVI 379

Query: 457 AMDGGLFEHHVRYRSYMEEALQELMGSDAAYEVALRLQNDGSGIGAALLAA 507
            +DG LFE    Y S +   L+E+  +D A  +   L  +GSGIGAA+ AA
Sbjct: 380 GLDGSLFEKMPGYLSKVRAVLREVF-NDKAQSILPVLTGNGSGIGAAIAAA 429


Lambda     K      H
   0.318    0.135    0.388 

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: 440
Number of extensions: 26
Number of successful extensions: 9
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: 513
Length of database: 436
Length adjustment: 33
Effective length of query: 480
Effective length of database: 403
Effective search space:   193440
Effective search space used:   193440
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 (21.7 bits)
S2: 51 (24.3 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