Alignments for a candidate for gudD in Pantoea rwandensis LMG 26275

GapMind for catabolism of small carbon sources

Alignments for a candidate for gudD in Pantoea rwandensis LMG 26275

Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate WP_084936388.1 HA51_RS20305 glucarate dehydratase

Query= SwissProt::P42206
         (451 letters)



>NCBI__GCF_002095475.1:WP_084936388.1
          Length = 448

 Score =  600 bits (1547), Expect = e-176
 Identities = 296/442 (66%), Positives = 350/442 (79%), Gaps = 5/442 (1%)

Query: 13  APVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGIRKTLE 72
           +PVITD++V+PVAG+DSMLLN+ GAH   FTRNI++LTDS GH GVGE PGGE I +TL 
Sbjct: 6   SPVITDMQVIPVAGYDSMLLNIGGAHSACFTRNIVVLTDSDGHTGVGEAPGGETIYQTLV 65

Query: 73  DARHLLINQSIGNYQSLLNKVR--NAFADRDVGGRGLQTFDLRIAVHAVTAVESALLDLL 130
           +A   +  Q +     L+ +V   N  AD D  G+G  TF+LR  V+AV A+E+ALLDLL
Sbjct: 66  EAIPQVKGQQVARMNRLVQQVHKGNQSADFDTFGKGAWTFELR--VNAVAALEAALLDLL 123

Query: 131 GQHLQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKEALT 190
           GQ L VPVA LLG GQQRD V +LGYLFY+GDR KTDL Y +   A ++W+ LR++EALT
Sbjct: 124 GQCLGVPVAELLGPGQQRDEVTVLGYLFYLGDRRKTDLPYLTGEGASHDWYHLRHQEALT 183

Query: 191 PESVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWSLKE 250
           PE+VV LAEAA D+YGFKDFKLKGGVL GE EI +  AL +RFPDARIT+DPNGAW+L E
Sbjct: 184 PEAVVRLAEAAQDKYGFKDFKLKGGVLPGEQEIESAAALKKRFPDARITVDPNGAWTLDE 243

Query: 251 AVALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHAIQL 310
           A+ LC+    VL YAEDPCGAE GYSGREVMAEFRR+TGL  ATNMIAT+WR+M HA+ L
Sbjct: 244 AIRLCKGMGDVLTYAEDPCGAEQGYSGREVMAEFRRATGLPVATNMIATNWREMNHAVML 303

Query: 311 QSVDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGNITA 370
            SVDIPLADPHFWT  G+VRVAQ+C++WGLTWG HSNNHFDISLAMFTHV AAAPG  TA
Sbjct: 304 NSVDIPLADPHFWTPSGAVRVAQLCDDWGLTWGCHSNNHFDISLAMFTHVGAAAPGKPTA 363

Query: 371 IDTHWIWQDG-QRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGARDD 429
           IDTHWIWQ+G QRLTKEPLQI+ G + VP KPGLGVELDWD L +A+ +YKS+  G+R+D
Sbjct: 364 IDTHWIWQEGDQRLTKEPLQIRNGKIAVPDKPGLGVELDWDRLHQANALYKSLPAGSRND 423

Query: 430 ATAMRYLVSGWEFNNKRPCMVR 451
           ATAM+YLV GW F+ KRP   R
Sbjct: 424 ATAMQYLVPGWSFDRKRPAFGR 445


Lambda     K      H
   0.319    0.135    0.410 

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: 629
Number of extensions: 17
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: 451
Length of database: 448
Length adjustment: 33
Effective length of query: 418
Effective length of database: 415
Effective search space:   173470
Effective search space used:   173470
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: 51 (24.3 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:

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 2024 update 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