Alignments for a candidate for xad in Marivita geojedonensis DPG-138

GapMind for catabolism of small carbon sources

Alignments for a candidate for xad in Marivita geojedonensis DPG-138

Align Dihydroxyacid dehydratase/phosphogluconate dehydratase protein; EC 4.2.1.9 (characterized, see rationale)
to candidate WP_085640705.1 MGEO_RS17335 dihydroxy-acid dehydratase family protein

Query= uniprot:D8IWS7_HERSS
         (594 letters)



>NCBI__GCF_002115805.1:WP_085640705.1
          Length = 593

 Score =  791 bits (2042), Expect = 0.0
 Identities = 386/586 (65%), Positives = 470/586 (80%)

Query: 9   RRFRSQDWFDNPDHIDMTALYLERFMNYGITAEELRSGRPIIGIAQSGSDISPCNRIHLE 68
           +RFRSQ+WFDNP++  MTALYLER+ N   T  EL++ +PIIGIA +GSD++PCN+IH+ 
Sbjct: 8   KRFRSQEWFDNPNNPGMTALYLERYQNQSFTQGELQAEKPIIGIANTGSDLAPCNKIHVF 67

Query: 69  LAKRVRDGIRDAGGIPMEFPLHPIFENCRRPTAAIDRNLAYLGLVEILHGYPIDAVVLTT 128
           L  R++ GIRD GGIPMEFP+HPI E  +RPTAA+DRNLAYL LVE+LHGYPID VVLTT
Sbjct: 68  LMDRIKAGIRDGGGIPMEFPVHPIQETGKRPTAALDRNLAYLSLVEVLHGYPIDGVVLTT 127

Query: 129 GCDKTTPSQIMAAATVDIPAIVLSGGPMLDGWMDGELVGSGSAIWKGRKLLSAGSIDNEK 188
           GCDKTTP+Q+M AATVDIPAI L+GGPMLDGW  G+  GSG+ IW+GR+L++ G I   +
Sbjct: 128 GCDKTTPAQLMGAATVDIPAIALNGGPMLDGWYKGKRAGSGTTIWEGRRLMARGEIGYGE 187

Query: 189 FLEIAAASAPSSGHCNTMGTASTMNAMAEALGMSLTGCSAIPAPYRERGQMAYETGRRIV 248
           F+++A AS+PS GHCNTMGTASTMNAMAEALGM+L G SAIPAP+RER  MAYETG+R V
Sbjct: 188 FMDLACASSPSLGHCNTMGTASTMNAMAEALGMTLPGSSAIPAPFRERMAMAYETGKRCV 247

Query: 249 GMAYEDLRPSAILTRDAFLDAIVVNAAIGGSTNAQPHIMAMARHAGVELQSEDWMKYGYD 308
            M  +DL+PS ILTR+AF +AIVVNAAIGGSTNA PH+ A+ARHAGVEL   DW K G+D
Sbjct: 248 QMVLDDLKPSNILTREAFENAIVVNAAIGGSTNAPPHLQAIARHAGVELDVTDWEKIGFD 307

Query: 309 VPLLLNMQPAGKYLGERFHRAGGVPAIMWELQQAGKLRAERITATGKTMAENLQGRASND 368
           VPL++NMQPAG+YLGE F+RAGGVPA+M EL++AG+L    +TA+G+ + + L    S D
Sbjct: 308 VPLMVNMQPAGEYLGESFYRAGGVPAVMGELRKAGRLHEGVMTASGQRLGDVLASWESLD 367

Query: 369 REMIYPFAAPLRERAGFLVLKGNLFDFAIMKTSVISETFRERYLSTPGQENIFECRAVVF 428
           R++I  + APLR++AGF VL GNLFD A+MKTSVIS  FR+R+LS PG+E +FE RA+VF
Sbjct: 368 RDVITTYDAPLRDKAGFKVLSGNLFDSALMKTSVISADFRKRFLSKPGEEGVFEARAIVF 427

Query: 429 DGSDDYHARINDPALKIDENTLLAIRGAGPVGWPGSAEVVNMQPPDALIKRGVSTLPTLG 488
           +G +DYH RINDP L IDEN +L IR  G VG+PGSAEVVNMQPPDAL+K G++ LPT+G
Sbjct: 428 EGPEDYHDRINDPDLAIDENCILFIRNVGCVGYPGSAEVVNMQPPDALVKAGINHLPTVG 487

Query: 489 DGRQSGTSDSPSILNASPESAVGGGLAYLRDGDRVRIDLNTGECNMLVSEEELARRKSEG 548
           DGRQSGTS+SPSILNASPE+ VGGGLAYL+ GDRVR+DLN    N LV E E   RK+  
Sbjct: 488 DGRQSGTSESPSILNASPEAVVGGGLAYLQTGDRVRLDLNASTLNALVDEAEWEARKAAW 547

Query: 549 IPPVPPSQTPWQEIYRSTVGQLETGACMELALKYQGVAQTLPRHNH 594
             P   +QTPWQEIYR  VGQL  G C+ELA  YQ +A+ LPR NH
Sbjct: 548 EAPEIVNQTPWQEIYRRHVGQLADGGCLELATAYQRIARDLPRDNH 593


Lambda     K      H
   0.318    0.135    0.405 

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: 1135
Number of extensions: 42
Number of successful extensions: 1
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: 594
Length of database: 593
Length adjustment: 37
Effective length of query: 557
Effective length of database: 556
Effective search space:   309692
Effective search space used:   309692
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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