Alignments for a candidate for uxaC in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for uxaC in Sinorhizobium meliloti 1021

Align Uronate isomerase; EC 5.3.1.12; Glucuronate isomerase; Uronic isomerase (uncharacterized)
to candidate SM_b21354 SM_b21354 glucuronate isomerase

Query= curated2:Q8YCQ2
         (466 letters)



>FitnessBrowser__Smeli:SM_b21354
          Length = 469

 Score =  614 bits (1583), Expect = e-180
 Identities = 295/465 (63%), Positives = 361/465 (77%), Gaps = 1/465 (0%)

Query: 3   LNPDRLFSAEPGTREIARRLFASVEKLPIISPHGHTEPIWYARNEAFPDPASLFVKPDHY 62
           ++PD LF AE  TR +ARRL+A V  LPI+SPHGHTEP WYA +EAFPDPA L + PDHY
Sbjct: 5   IDPDLLFPAEERTRALARRLYAEVSGLPIVSPHGHTEPRWYALDEAFPDPAQLLIVPDHY 64

Query: 63  ITRMLYSQGHSLESLGIASRDGRPSETDARKIWRLFATNWYLFRATPSRLWFEHAMETVF 122
           + RML+SQG  LE LG+ + DG P ETD R IWR F  N++LFR TP+RLWF++ +  +F
Sbjct: 65  VFRMLFSQGIRLEELGVPALDGSPVETDGRAIWRRFCENYHLFRGTPTRLWFDYTLSELF 124

Query: 123 GITERLSQENADRIFDAIADQLTQPHMRPRALYDRFNIEAISTTDAATDPLIYHDEVIAS 182
           GI E  S  ++D ++D +A+ LT+P  RPRALY+RFNIE ISTTD+A D L +H +++ S
Sbjct: 125 GIDELPSAASSDPLYDHVAECLTRPDYRPRALYERFNIEVISTTDSALDDLGWHAKILES 184

Query: 183 GWHGRIIPAYRPDAAVDAGRPDFASEVEKLVGVAGTPL-TWQGYLDAHRNRREYFKRRGA 241
           GW GR++PAYRPDA VD     F + ++KL  + G    TW GYLDAHR RR YFK  GA
Sbjct: 185 GWKGRVVPAYRPDAVVDPDFQGFPTNLDKLGDITGADTGTWSGYLDAHRTRRAYFKDFGA 244

Query: 242 TSSDHGHPTAQTADLSAGDASRLFDRVIKGNASTSDAEMFRAQMLTEMARMSIDDGLVMQ 301
           TS+DHGH TA TA+L   +A+ LFD+V  G A+  +  +FRAQMLTEMA+MS+DDGLVMQ
Sbjct: 245 TSTDHGHATADTANLPQAEAAALFDKVRLGKANADERRLFRAQMLTEMAKMSLDDGLVMQ 304

Query: 302 IHPGSFRNHNPTVFERFGLDKGADIPRQTGFVDQLKPLLDAFGNDPRLTVILFTLDETAL 361
           IHPGSFRNH+P +  +FG DKG DIP +T +V  LKPLLDA G +  LTVILFTLDET+ 
Sbjct: 305 IHPGSFRNHSPAILAKFGRDKGFDIPTRTDYVTALKPLLDAVGLERDLTVILFTLDETSY 364

Query: 362 SRELAPLAGHYPALKLGPAWWFFDSPEGILRYRKLTTETAGFYNTVGFNDDTRAYLSIPA 421
           +RELAPLAG YPALKLGPAWWF DS EG+ R+R++TTETAGFYNTVGFNDDTRA+ SIPA
Sbjct: 365 ARELAPLAGVYPALKLGPAWWFHDSAEGMRRFREMTTETAGFYNTVGFNDDTRAFPSIPA 424

Query: 422 RHDMARRVDCAYLAGLVADHRLEEDEAYEVAHDLAYRLAKQTYKL 466
           RHD+ARRVDCA+LA LVA+HRL EDEAYE+A DLAY LAK+ Y+L
Sbjct: 425 RHDIARRVDCAFLARLVAEHRLREDEAYELARDLAYGLAKEAYRL 469


Lambda     K      H
   0.321    0.136    0.418 

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: 819
Number of extensions: 31
Number of successful extensions: 3
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: 466
Length of database: 469
Length adjustment: 33
Effective length of query: 433
Effective length of database: 436
Effective search space:   188788
Effective search space used:   188788
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources