GapMind for Amino acid biosynthesis

 

Alignments 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:

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:

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:

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:

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