GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Korea:Ga0059261_2969 Ga0059261_2969 Glucuronate
           isomerase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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