GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxaE in Gracilibacillus halophilus YIM-C55.5

Align tagaturonate epimerase (EC 5.1.2.7) (characterized)
to candidate WP_003470005.1 J416_RS09955 hypothetical protein

Query= BRENDA::Q9WYS1
         (481 letters)



>NCBI__GCF_000359605.1:WP_003470005.1
          Length = 504

 Score =  355 bits (911), Expect = e-102
 Identities = 202/476 (42%), Positives = 283/476 (59%), Gaps = 18/476 (3%)

Query: 16  VYEKSYREKDSLSFFLTKEEEGKILVVAGEKAPEGLSFFKKQRAEGVSFF-FCERNHENL 74
           VY  S+ E       + K    K++V AG         F+    E +     C   HEN 
Sbjct: 26  VYTPSFEEHAGSQVVMVKSGTEKMIVAAGAG-----ELFEALSGEDIGKGKVCPLTHENR 80

Query: 75  EVLRKYFPDLKPVRAGLR-ASFGTGDRLGITTPAHVRALKDSGLFPIFAQQSVRENERTG 133
            VL ++F    P   G   A+ G GDRLGI +P H+  +K+  + PI AQQS+RE     
Sbjct: 81  LVLNQFFSYTAPQAFGTDIATMGLGDRLGIASPGHIDTVKERNVKPILAQQSIRELTLLN 140

Query: 134 RTWRDVLDDATWGVFQEGYSEGFGADADHVKRPEDLVSAAREGFTMFTIDPSDHVRN-LS 192
           RT  D+LD A + VFQEGY +G+GADADH+K   D+  A + GF+  T+D S+ +RN + 
Sbjct: 141 RTMTDILDAAAFAVFQEGYKDGYGADADHIKLESDIEHALQLGFSFLTLDCSEQIRNDVE 200

Query: 193 KLTEKERNEKFEEILRKER--IDRIYLGKKYSVLGEKIEFDEKNLRDAALVYYDAIAHVD 250
             T  E   +F  +  ++R      YL + ++V   +I FD+ NL    LVY +AI  ++
Sbjct: 201 SQTSDEIQNEFASLSDEKRAYFSNYYLDQTFNVHERQISFDQANLAKNVLVYGEAIDFME 260

Query: 251 MMYQI-LKDETPDFDFEVSVDETETPTSPLFHIFVVEELRRRGVEFTNLALRFIGEWEKG 309
            +Y   L+    D DFE+S+DETET TSP  H FV EELRRRGV+  +LA RF GE++KG
Sbjct: 261 HVYHTYLQSLDRDVDFEISIDETETVTSPEAHFFVAEELRRRGVKVESLAPRFCGEFQKG 320

Query: 310 IDYKGDLAQFEREIKMHAEIARMFEGYKISLHSGSDKFSVYPAFASATGGLFHVKTAGTS 369
           IDY GD+ QFE+E+K HA+IA+ F GYK+S+HSGSDKFSV+P     T GL H+KTAGT+
Sbjct: 321 IDYIGDMDQFEKELKEHADIAKHF-GYKLSIHSGSDKFSVFPIIGKYTDGLLHIKTAGTN 379

Query: 370 YLEAVKVISMVNPELFREIYRCTLDHFEEDRKSYHISADLSKVPEVEKVKDEDLPGLFED 429
           +LEAV+V++  NP+L+R ++    +HFEE  K YH++ DL  V  +++  D+ LP     
Sbjct: 380 WLEAVRVVAQENPDLYRRMHVYAEEHFEETLKYYHVTPDLDSVTPLKEQPDDQLPEYMNH 439

Query: 430 INVRQLIHVTYGSVL--KDAS----LKERLFKTLEQNEELFYETVAKHIKRHVDLL 479
              RQL HVTYG +L  KD +     ++  F TL   E+ + + +A HI RH+DLL
Sbjct: 440 DAARQLFHVTYGILLTAKDDAGNDLFRDEFFDTLLNKEDAYRQALAHHIGRHLDLL 495


Lambda     K      H
   0.320    0.138    0.398 

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: 742
Number of extensions: 40
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: 481
Length of database: 504
Length adjustment: 34
Effective length of query: 447
Effective length of database: 470
Effective search space:   210090
Effective search space used:   210090
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: 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