GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylB in Lentibacillus jeotgali Grbi

Align Xylulose kinase; Short=Xylulokinase; EC 2.7.1.17 (characterized, see rationale)
to candidate WP_010531875.1 ON01_RS14910 xylulose kinase

Query= uniprot:Q97FW4
         (500 letters)



>NCBI__GCF_000224785.1:WP_010531875.1
          Length = 496

 Score =  211 bits (538), Expect = 4e-59
 Identities = 154/504 (30%), Positives = 238/504 (47%), Gaps = 19/504 (3%)

Query: 3   YLLGIDVGTSGTKTALFDECGNTIKTSTHEYELFQPQVGWAEQNPENWWTACVKGIREVI 62
           Y    D+GT+  K AL     +     T E E      G  EQNP +WW        +  
Sbjct: 4   YAAVFDIGTTAVKGALVRNDASFYSERTVELETHYAPDGIVEQNPNDWWDGVKFIAHQWW 63

Query: 63  EKSKIDPLDIKGIGISGQMHGLVLIDKEYKVIRNSIIWCDQRTEKECTQITDTIGKEKLI 122
           +++ +DP  +  I  +GQM  ++ I  +++ +  +I++ D R   E   +       +++
Sbjct: 64  KEAGVDPGQVAIISFTGQMEDVIPIT-QHQTVNRAILYSDTRAVSEAEWLHQQF--PEMV 120

Query: 123 RITGNPALTGFTLSKLLWVRNNEPDNYKRIYKVLL-PKDYIRFKLTGVFAAEVSDASGTQ 181
           ++TGNP      L+KLL ++N     Y      L   KD++ ++LTG  A + + A+ T 
Sbjct: 121 QMTGNPISATTPLAKLLQMKNRNQKIYDDTRCFLFGSKDFMIYRLTGAIATDPTTAATTG 180

Query: 182 MLDINTRNWSEELLDDLRIDKNILPDVYESVVVSGCVIEKASKETKLAVNTPVVGGAGDQ 241
           M+D+ TR W  ++     ID   LP + ++    G V ++A+ ET     TPV+ G GD 
Sbjct: 181 MMDVRTRRWETDIFSLTGIDTEKLPRILDAADPVGYVHKEAALETGFRPETPVLCGCGDA 240

Query: 242 AAGAIGNGIVREGLISTVIGTSGVVFAATD--TPRFDSKGRVHTLCHAVPNKWHIMGVTQ 299
           AA AIG G V+ G     IGT+G +    +   P   S G  H L H        +    
Sbjct: 241 AASAIGAGAVKSGDSYCYIGTTGWIAGIQEDVNPEAASHGLFH-LAHLPEKSIISVAPLL 299

Query: 300 GAGLSLNWFKRTFCAKEILESKEAGINIYDLLTEKASQSKPGSNGIIYLPYLMGERTPHI 359
            AG    W   TF   ++ +   A    ++ L     QS PGSNG+++LPYL GER P  
Sbjct: 300 NAGNVYQWGADTFAEGQVNDRFHA----FEALIR---QSAPGSNGVLFLPYLQGERNPVN 352

Query: 360 DPNVKGAFLGISLINNHNDFVRSILEGVGFSLKNCLDIIENMKVNIEEIRVSGGGAESSI 419
           D   KGAF GI       D  R+I+EG+ FSLK  ++++ N++ N + +   GGG +SS 
Sbjct: 353 DQQAKGAFWGIGPQTKKCDLARAIIEGICFSLKQVMEVL-NLESN-DVLTTVGGGTKSST 410

Query: 420 WRQILSDIFNYELTTV-KASEGPALGVAILAGVGAGIYNSVEEACDKIVK--GNEKVMPN 476
           W Q L+DI    +    + S   ALG    A +  G  N  E+  D+ +    +E   P+
Sbjct: 411 WCQTLADILERPVRIAPENSYMSALGAVSPAFLQLGWTNDYEDFTDRFINMPVSEIFEPS 470

Query: 477 ANLIEVYSKVYEVYNSAYPKIKDI 500
            N   VY   Y+ +   YP +K I
Sbjct: 471 QNTFAVYRDQYKQFLKMYPGLKGI 494


Lambda     K      H
   0.317    0.136    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: 544
Number of extensions: 21
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: 500
Length of database: 496
Length adjustment: 34
Effective length of query: 466
Effective length of database: 462
Effective search space:   215292
Effective search space used:   215292
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: 52 (24.6 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