GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpK in Lactobacillus silagei IWT126

Align Glycerol kinase; EC 2.7.1.30; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK (uncharacterized)
to candidate WP_089137208.1 CES79_RS10945 gluconokinase

Query= curated2:Q7NC65
         (508 letters)



>NCBI__GCF_002217945.1:WP_089137208.1
          Length = 520

 Score =  172 bits (435), Expect = 3e-47
 Identities = 141/484 (29%), Positives = 225/484 (46%), Gaps = 25/484 (5%)

Query: 6   YIITLDEGTTSCRSIVFDKQAKIVSVAQNEFTQYFPQSGWVEHDPLEIWNTQLSTMQSVK 65
           Y+I +D GTTS ++++FD   K+   + N +  Y       E DP EI++  +  + +V 
Sbjct: 3   YMIGVDIGTTSVKTVLFDNVGKVQGYSNNLYPLYQDVPDMAEEDPDEIFSAIVDGLTTVL 62

Query: 66  NKAQIKSVNVEAVGITNQRETVVLWNKETGLPVYNAIVWQDRRTSEYCETLTKHV--DKV 123
            KA +    ++ V  +    +++L + E   P+  AI W D R  +Y + L ++    ++
Sbjct: 63  RKANLSKGELKGVSFSAAMHSLILLD-ENHKPMTRAITWADNRAVKYADQLRENGVGKQI 121

Query: 124 REKTGLIINPYFSGTKIRWILKNVPLAQKTLKAGKLLAGTIDSWLIWKLTGGKVHATDVS 183
            EKTG  I+P    TK+ W+       +      +   G I  ++I+KL G  V   D S
Sbjct: 122 YEKTGTPIHPMTPFTKLIWLRNE---HKDLFDKARWFVG-IKEYVIYKLFG--VLKEDYS 175

Query: 184 NASRTLLFNIHTMDWDQELLDLFEIPRSILPE-VKSSSEVYGYVEPSLWSQRATAKVPIT 242
            A+ T +FNI  MDWD + L+L  + R  LPE V ++  V G  E            P  
Sbjct: 176 IANATGMFNIFKMDWDDQALELAGVTRDKLPELVDTTDTVSGMNEDYARVIGIDPDTPFV 235

Query: 243 GVAGDQQSALFGQLCLKPGMVKNTYGTGCFTLMNIGEKPIMSKNKLLTTVAWKLGKKKPV 302
             A D   A  G   + PG+V  T GT     +   +  I  K ++     + L   K  
Sbjct: 236 MGASDGPLANLGVNAIDPGVVAVTIGTSGAVRVVTDKPKIDPKGRVF---CYYLAPGK-- 290

Query: 303 YALEGSVFIAGAAVQWIRDGL----RLIYDAAESDFY---ANLASKQDTHQVYLV--PSF 353
           + + G V   G   +W+RD L    ++  +  + D Y     +ASK       L+  P  
Sbjct: 291 WVVGGPVNNGGIVFRWVRDQLFAPEKITAEQMKIDSYDLLTEIASKIPAGSDGLIFHPFL 350

Query: 354 TGLGAPYWDSYSRGAIFGLERGTKKEHIIKATLESIVFQTNDLIKAMSSDVGKKIEVVKV 413
            G  AP WD+ +RG+ FGL R   + H+++A LE IV+    ++ A+   VGK +  ++ 
Sbjct: 351 GGERAPIWDANARGSFFGLTRKHTRAHMVRAALEGIVYNLYTVLIALEEVVGKPVS-IQA 409

Query: 414 DGGATRSEYIMQFQSSISGVNVIRPKNIESTALGATFLAGLAVGYWKDLKELEKLVKVDK 473
            GG  RS    Q  + I   +V  P+++E TALGA  L   ++G   DL E++K V V  
Sbjct: 410 TGGFARSALWRQMLADIFEQDVTIPESVEGTALGAAVLGMYSLGLIDDLSEVKKFVGVTN 469

Query: 474 EFKP 477
              P
Sbjct: 470 VHHP 473


Lambda     K      H
   0.317    0.133    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: 571
Number of extensions: 34
Number of successful extensions: 5
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: 508
Length of database: 520
Length adjustment: 35
Effective length of query: 473
Effective length of database: 485
Effective search space:   229405
Effective search space used:   229405
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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