GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxaC in Sphingomonas koreensis DSMZ 15582

Align Uronate isomerase; EC 5.3.1.12; Glucuronate isomerase; Uronic isomerase (uncharacterized)
to candidate Ga0059261_2969 Ga0059261_2969 Glucuronate isomerase

Query= curated2:Q1GNM2
         (470 letters)



>FitnessBrowser__Korea:Ga0059261_2969
          Length = 479

 Score =  640 bits (1652), Expect = 0.0
 Identities = 315/472 (66%), Positives = 365/472 (77%), Gaps = 8/472 (1%)

Query: 3   RPLYLSPDRLFPSDPAQRDIARRLYKAVAGLPIVSPHGHTDPAWFAGDAPFGNAAELLLH 62
           RPL L PDRLFP++P  R IA  LYK +AGLPIVSPHGHTDP+WFA D  + NA EL L 
Sbjct: 2   RPLALDPDRLFPAEPTTRAIACDLYKEIAGLPIVSPHGHTDPSWFATDDAWENATELFLA 61

Query: 63  PDHYVFRMLYSQGVSLDALGIGNADA----DPRESWRLFAENYHLFRATPSRMWMDWVFA 118
           PDHYVFRMLYSQGV LDAL +   D     DPR +WRLFA NYHLFR TPSRMW+D VFA
Sbjct: 62  PDHYVFRMLYSQGVDLDALRVPRIDGVPATDPRAAWRLFASNYHLFRGTPSRMWLDHVFA 121

Query: 119 EVFGFDVQLSAETSDLYYDRITEALAIDAFRPRALFDRFGIEVIATTESPLDSLDHHAVI 178
           EVFG +  L + T+D YYD I EALA  A+RPRALF+RF I+ +ATTE   D L+HHA I
Sbjct: 122 EVFGIERLLDSGTADHYYDTINEALATPAYRPRALFERFKIDFLATTEGADDPLEHHAAI 181

Query: 179 RAANASGEWGGRVITAYRPDPVVDPEFEGFRDNLARFSNLSGEDAFSYSGYLAAHRKRRA 238
           R +     WGGRV+T YRPD V+D E E F+  L  F+ L+GED  S+ GYLAAHRKRRA
Sbjct: 182 RRSG----WGGRVVTTYRPDSVIDVEHEAFKGALEAFAGLTGEDVHSWKGYLAAHRKRRA 237

Query: 239 FFASMGATSTDHGHPSAATADLSETQAEALFARVTGEDMSAADAELFRAHMLTVMAGMSL 298
            F   GAT+TDHG  +A TA+LS  ++EALF R+      AADAELFRA MLT MA MS+
Sbjct: 238 DFRIAGATATDHGFATAQTANLSTAESEALFGRIMSGKWDAADAELFRAQMLTEMAKMSV 297

Query: 299 DDGLVMQIHPGAFRNHNPWLFANHGRDKGADIPTATDYVHALRPLLGRYGNEADLTIILF 358
           +DG+ MQIHPGA RNHN  LF +HGRDKGADIPT TDYVHAL+P+L   GNE  LT+ILF
Sbjct: 298 EDGMTMQIHPGACRNHNAKLFHSHGRDKGADIPTRTDYVHALKPMLDVVGNEPGLTVILF 357

Query: 359 TLDETSYARELAPLAGHYPALKLGPAWWFHDSPEGMRRFRSQMTETAGFYNTVGFNDDTR 418
           TLDE++YARELAPLAGHYP L+LGP+WWFHDSPEGMRRFR   TETAGFYNTVGFNDDTR
Sbjct: 358 TLDESTYARELAPLAGHYPCLRLGPSWWFHDSPEGMRRFREMTTETAGFYNTVGFNDDTR 417

Query: 419 AFLSIPARHDVARRIDCGFLAQLVSEHRLEEWEAAELAADLSYNLAKASYKL 470
           AF SIPARHDVARR+DC FLA+LV+E R+++WEAAELA +L+  L + +YKL
Sbjct: 418 AFFSIPARHDVARRVDCAFLARLVAEGRMQDWEAAELAYELTNGLVRKAYKL 469


Lambda     K      H
   0.322    0.136    0.423 

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: 817
Number of extensions: 27
Number of successful extensions: 4
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: 470
Length of database: 479
Length adjustment: 33
Effective length of query: 437
Effective length of database: 446
Effective search space:   194902
Effective search space used:   194902
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 (21.9 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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