Alignments for a candidate for ilvD in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Caulobacter crescentus NA1000

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate CCNA_00862 CCNA_00862 xylonate dehydratase xylD

Query= curated2:A5UY13
         (559 letters)



>FitnessBrowser__Caulo:CCNA_00862
          Length = 591

 Score =  283 bits (724), Expect = 1e-80
 Identities = 200/548 (36%), Positives = 279/548 (50%), Gaps = 29/548 (5%)

Query: 29  GFTDEDL--AKPIIGIANTWIETMPCNINLRALAARVKEGVRAAGGTPMEFNTVAIADGV 86
           G T E+L   KPIIGIA T  +  PCN     L  RV++G+R AGG PMEF    I +  
Sbjct: 35  GITPEELRSGKPIIGIAQTGSDISPCNRIHLDLVQRVRDGIRDAGGIPMEFPVHPIFENC 94

Query: 87  TMGTEGMKASLISRDLIADSIELMGRGYMFDAIIALVACDKTIPGAAMGLTRLNIPGFLL 146
              T  +  +L    L+         GY  DA++    CDKT P   M  T +NIP  +L
Sbjct: 95  RRPTAALDRNLSYLGLVETL-----HGYPIDAVVLTTGCDKTTPAGIMAATTVNIPAIVL 149

Query: 147 YGGSIAPGHWRGKEITIQH--VYEAIGAVAAGKMTDEELKEIEDAACPGPGACGGQYTAN 204
            GG +  G W   E+      ++ +   +AAG++T+EE  +   ++ P  G C    TA+
Sbjct: 150 SGGPMLDG-WHENELVGSGTVIWRSRRKLAAGEITEEEFIDRAASSAPSAGHCNTMGTAS 208

Query: 205 TMATVMEIIGLSPMGTAAVPAADPRKDSVGYRAGQLIMDVLRRDLKPRDILTRAAFENAI 264
           TM  V E +GLS  G AA+PA    +  + Y+ GQ I+D+   D+KP DILT+ AFENAI
Sbjct: 209 TMNAVAEALGLSLTGCAAIPAPYRERGQMAYKTGQRIVDLAYDDVKPLDILTKQAFENAI 268

Query: 265 ASVALTGGSTNAVLHLLALAREAGVPLTLDDFDAISRRTPLCCDLMPSGKYSAIHVDQAG 324
           A VA  GGSTNA  H++A+AR AGV +T DD+ A +   PL  ++ P+GKY      +AG
Sbjct: 269 ALVAAAGGSTNAQPHIVAMARHAGVEITADDWRA-AYDIPLIVNMQPAGKYLGERFHRAG 327

Query: 325 GIQVIARRLVDGGFAHGDAITVTGRTLAEEAADAVETPGQDVIRPLDNPIKPTGGLLVLR 384
           G   +   L+  G  HGD +TVTG+T++E      ET  ++VI P   P+    G LVL+
Sbjct: 328 GAPAVLWELLQQGRLHGDVLTVTGKTMSEN-LQGRETSDREVIFPYHEPLAEKAGFLVLK 386

Query: 385 GNL---APEGSVVKLFGYERTYHRGP---------ARVFDGEEAAMAAIVGGEIRPDD-- 430
           GNL   A   S V    + + Y   P         A VFDG +     I    +  D+  
Sbjct: 387 GNLFDFAIMKSSVIGEEFRKRYLSQPGQEGVFEARAIVFDGSDDYHKRINDPALEIDERC 446

Query: 431 IVIIRYEGPRGGPGMREMLGV--TSAIVGAGLGQSVSLITDGRFSGATRGVMIGHVAPEA 488
           I++IR  GP G PG  E++ +     ++  G+  S+  + DGR SG      I + +PE+
Sbjct: 447 ILVIRGAGPIGWPGSAEVVNMQPPDHLLKKGI-MSLPTLGDGRQSGTADSPSILNASPES 505

Query: 489 ARGGPLAIVQEGDEIEINLDERRVDLLLSEEEIADRLLAWQPPAPRYEWGVMARYGALVS 548
           A GG L+ ++ GD I I+L+  R D L+ E  IA R     P  P         Y A  S
Sbjct: 506 AIGGGLSWLRTGDTIRIDLNTGRCDALVDEATIAARKQDGIPAVPATMTPWQEIYRAHAS 565

Query: 549 SASEGAVL 556
               G VL
Sbjct: 566 QLDTGGVL 573


Lambda     K      H
   0.319    0.137    0.401 

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: 837
Number of extensions: 43
Number of successful extensions: 7
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: 559
Length of database: 591
Length adjustment: 36
Effective length of query: 523
Effective length of database: 555
Effective search space:   290265
Effective search space used:   290265
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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
changes to Amino acid biosynthesis since the original publication.

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 Amino acid biosynthesis