GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Dinoroseobacter shibae DFL-12

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate 3606698 Dshi_0129 dihydroxy-acid dehydratase (RefSeq)

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Dino:3606698
          Length = 577

 Score =  228 bits (580), Expect = 7e-64
 Identities = 171/547 (31%), Positives = 265/547 (48%), Gaps = 40/547 (7%)

Query: 32  SDGPQRGKLQCANFAHGVAGCGSEDKHSLRMMNAANVAIVSSYNDMLSAHQPYEHFPEQI 91
           ++GP R   +   +A G+     E+ H         V + + +N+    +       + +
Sbjct: 17  TEGPSRAPHRSYYYAMGMT---EEEIHQ------PLVGVATCWNEAAPCNIALSRQAQAV 67

Query: 92  KKALREM-GSVGQFAGGTPAMCDGVTQGEAGMELSLPSREVIALSTAVALSHNMFDAALM 150
           K  +++  G+  +F   T  + DG+  G  GM  SL SRE IA +  + +  + +DA + 
Sbjct: 68  KMGVKQASGTPREFT--TITVTDGIAMGHEGMRSSLASREAIADTVELTMRGHCYDAIVG 125

Query: 151 LGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGISNKEKADVRQ------RYAEGKATR 204
           L  CDK +PG+MM  +R  ++P++F+ GG +  G  N E   V+       ++  G  T 
Sbjct: 126 LAGCDKSLPGMMMAMVRL-NVPSVFIYGGSILPGRLNGEDVTVQDVFEAVGKHQAGNYTD 184

Query: 205 EELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLPGASFVNPYTPLRDALTHEAAQQ 264
            EL   E  +  S G C    TANT   + E +GL LP ++        RD     + + 
Sbjct: 185 AELEVLERVACPSAGACGGQFTANTMACVSEAIGLALPNSAGAPAPYESRDQYGEASGRA 244

Query: 265 VTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGSTNHTLHMPAIAQAAGIQLTWQDMA 324
           V  L ++        +IV  +SL N+   +  TGGSTN  LH+PAIA  AGI+ T QD+ 
Sbjct: 245 VMDLIEKG---IRARDIVTRKSLENAARIVACTGGSTNAGLHLPAIAHEAGIEFTLQDVC 301

Query: 325 DLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELLEAGLLHEDVNTVAGRGLSRYTQE 384
           D+    P    + P GK        AGG+  ++REL  AGL+HED  TV G  +     +
Sbjct: 302 DIFRDTPYFVDLKPGGKYVAKDMYEAGGVPVVMRELRRAGLIHEDCMTVTGYSIGEELDK 361

Query: 385 PFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGLRVMEGNLG--RGVMKVSAVALQHQ 442
             L+              D  ++ PV    S  GG+  +EGNL     ++K++ ++    
Sbjct: 362 VTLE-------------ADGRVIYPVDTPLSTTGGVVGLEGNLAPEGAIVKIAGMSDDQL 408

Query: 443 IVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRG 501
           +   PA VF+ ++D  +A +     +  V V+R +GP    GM E+   T  L   Q  G
Sbjct: 409 VFTGPARVFECEEDAFEAVQNRAYAEGDVFVIRNEGPAGGPGMREMLATTAALSG-QGMG 467

Query: 502 FKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADE 561
            KVAL+TDGR SGA+       HV PEA  GG +A ++DGD+I +D +KG L + +  DE
Sbjct: 468 KKVALITDGRFSGATRGFCVG-HVGPEAAHGGPIAMLKDGDMITIDALKGELSVALSEDE 526

Query: 562 FAAREPA 568
            AAR+ A
Sbjct: 527 LAARKDA 533


Lambda     K      H
   0.318    0.134    0.386 

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: 948
Number of extensions: 59
Number of successful extensions: 8
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: 608
Length of database: 577
Length adjustment: 37
Effective length of query: 571
Effective length of database: 540
Effective search space:   308340
Effective search space used:   308340
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 17 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:

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