Aligments for a candidate for ilvD in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvD in Marinobacter adhaerens HP15

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate GFF2220 HP15_2174 6-phosphogluconate dehydratase

Query= curated2:B1I250
         (569 letters)



>FitnessBrowser__Marino:GFF2220
          Length = 610

 Score =  245 bits (626), Expect = 3e-69
 Identities = 188/570 (32%), Positives = 279/570 (48%), Gaps = 53/570 (9%)

Query: 12  RAPHRSLLRATGII----------KDEADFQ-KPFVAIANSFAEIVPGHAHLNEFVKEIK 60
           ++PHRS L    +           KD   F  K  VA+  ++ +++  H    +F   I+
Sbjct: 37  QSPHRSSLSCGNLAHGFAACNQGDKDTLKFMNKANVAMVTAYNDMLSAHQPYEKFPDIIR 96

Query: 61  EAVREAGGVP-FEFNTLALCDGIAMNHPGMRYSLPSRELVADSVETMVQGHRFDGLICIP 119
           EA R  G V      T A+CDG+    PGM  SL SR+ +A S    +  + FD  + + 
Sbjct: 97  EAARGMGSVAQVAGGTPAMCDGVTQGQPGMELSLFSRDTIAMSTAVALSHNMFDATLLLG 156

Query: 120 NCDKIVPGMLMAAVRLN-IPTIFVSGGPMKAGRA-KDGRPIDLISVFEGIGAFRAGKIDA 177
            CDKIVPG+L+ ++    +PTI +  GPM +G   K+ + I  +        +  GK+  
Sbjct: 157 ICDKIVPGLLIGSLSFGYLPTILLPAGPMPSGLPNKEKQRIRQL--------YAEGKVGK 208

Query: 178 GDLLELEQAACPGYGSCAGMFTANSMNCLCEALGLALPGNGTILAVDPRRSELKKWAGRQ 237
            +LLE E  +    G+C    TANS   L E +GL +PG+  +    P R EL + A  Q
Sbjct: 209 EELLEAESKSYHSPGTCTFYGTANSNQLLVEVMGLHMPGSAFVNPNTPLRDELTRAATEQ 268

Query: 238 IVELIK---RDLRPRDIVTPEAIDNAFALDVAMGGSTNTILHLLAVAQEAGINYPLKRVN 294
           ++ L K    +L   D+V  ++I NA    +  GGSTN  +H +A+A+ AGI        
Sbjct: 269 VIRLSKPHGGELGLGDMVDEKSIVNALVALLVTGGSTNHTIHWIAIARAAGIIIDWNDYA 328

Query: 295 LISARTPTLCKISPASSLHIEDVDRAGGVSAVLGELSRKPGLLNLDCLTVTG-------- 346
            +S+  P++ +I P     +     AGG   ++ EL    G ++ D  TV G        
Sbjct: 329 ELSSVVPSMTRIYPNGQEDVNAFHEAGGTPFLIREL-LSGGYVHNDVNTVVGYGLERYTE 387

Query: 347 ------ETLGETVGQVQSLDPRVIRGVEEPLSPVGGLKVLFGSLAPEGAVVKTAAVVPQM 400
                 E L       +SL P V+  V EP +P GGL+VL G+L     V+K +AV P+ 
Sbjct: 388 MPELSDEQLVWKPAPEKSLRPDVLSPVAEPFAPDGGLRVLDGNLG--RGVIKVSAVAPEH 445

Query: 401 MRHQGPAVVFNSEAEASAAILGGRIKHGDVVVIRFEGPKGGPGFMEMLGPTAAL-VGMGL 459
            + + PAVVFN + E  AA   G +    +V++RF+GPK   G  E+   T  L V    
Sbjct: 446 RKVEAPAVVFNDQNELKAAFEAGDLDRDCIVIVRFQGPKSN-GMPELHKLTPYLGVLQDR 504

Query: 460 GESVALVTDGRFSG--GTRGACIGHVCPEAASGGPIALIKDGDLISYDLEAGTLELLVPQ 517
           G  V LVTDGR SG  G   A I HV PEA  GGP+A +K+GD++  D E+G L + +  
Sbjct: 505 GFKVGLVTDGRMSGASGKVPAAI-HVYPEALDGGPLAKVKNGDMVCLDAESGVLAIRLDD 563

Query: 518 EELAARKA------AFTPPLRQGLTGWLAR 541
           +E A R++       +     + L GW+ R
Sbjct: 564 QEFAGRESEKADLTGYHHGYGRELFGWMRR 593


Lambda     K      H
   0.319    0.138    0.409 

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: 955
Number of extensions: 65
Number of successful extensions: 9
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: 569
Length of database: 610
Length adjustment: 37
Effective length of query: 532
Effective length of database: 573
Effective search space:   304836
Effective search space used:   304836
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 Aug 03 2021. The underlying query database was built on Aug 03 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 paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the 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