GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Sphingomonas koreensis DSMZ 15582

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate Ga0059261_4216 Ga0059261_4216 Dihydroxyacid dehydratase/phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Korea:Ga0059261_4216
          Length = 573

 Score =  220 bits (561), Expect = 1e-61
 Identities = 172/542 (31%), Positives = 265/542 (48%), Gaps = 38/542 (7%)

Query: 32  SDGPQRGKLQCANFAHGVAGCGSEDKHSLRMMNAANVAIVSSYNDMLSAHQPYEHFPEQI 91
           S GP+R   +   +A G+    SE++ +        VA+ S+ ND    +   +   +  
Sbjct: 16  SVGPERAPHRSYYYAMGI----SEEEIARPF-----VALASAGNDSAPCNTTLDAQADAA 66

Query: 92  KKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLPSREVIALSTAVALSHNMFDAALML 151
           +K + + G + +    T  + DG+  G  GM+ SL SREVIA S  +++  + +DA +  
Sbjct: 67  RKGVADNGGLPR-RFNTITVTDGIAMGHQGMKSSLVSREVIADSVELSVRGHCYDALVGF 125

Query: 152 GICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG------ISNKEKADVRQRYAEGKATRE 205
             CDK +PG+MM  LR  ++P+IFV GG +  G      ++  +  +V  ++A G     
Sbjct: 126 AGCDKSLPGMMMAMLRL-NIPSIFVYGGSILPGRYQDRDVTVVDVFEVVGKFAAGTCPIS 184

Query: 206 ELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLPGASFVN-PYTPLRDALTHEAAQQ 264
           E+   E  +    G C    TANT   + E +GL LP ++ V  PYT  R+ +   A  Q
Sbjct: 185 EVHALEKVACPGHGACGGQYTANTMACVGEAIGLSLPNSNMVPAPYTS-REQIAVAAGYQ 243

Query: 265 VTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGSTNHTLHMPAIAQAAGIQLTWQDMA 324
           V  L ++  N  P  +I    + +N+   + ATGGSTN  LH+PA+A  AGI     D+A
Sbjct: 244 VMELLER--NIRP-RDICTREAFINAARIVAATGGSTNGALHLPAMASEAGIDFDLFDVA 300

Query: 325 DLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELLEAGLLHEDVNTVAGRGLSRYTQE 384
           ++ +  P  + + P GK        AGG+  L++ +LE GLL+ D  TV G+ L     +
Sbjct: 301 EVFKSTPYAADLKPGGKYVAKDMYEAGGVYMLMKSMLENGLLYGDCMTVTGKTLGENIDQ 360

Query: 385 PFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALQHQIV 444
                  + W        D+ ++  V    +P GG+  + G L      V    +   + 
Sbjct: 361 -------VTWNP------DQKVIYDVRTPITPTGGVVGLRGTLAPNGAIVKVAGMSRLVF 407

Query: 445 EAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFK 503
           E PA  F  ++D   A +  E+ +  V V+R++GP+   GM E+   T  L  L   G K
Sbjct: 408 EGPARCFDCEEDAFAAVEKREIREGEVVVIRYEGPKGGPGMREMLSTTAALYGL-GMGEK 466

Query: 504 VALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFA 563
           VAL+TDGR SGA+       HV PEA   G +A V DGD IR+D   GT++L V  D  A
Sbjct: 467 VALITDGRFSGATRGFCIG-HVGPEAAECGPIALVEDGDTIRIDAEAGTIDLHVAEDVLA 525

Query: 564 AR 565
            R
Sbjct: 526 ER 527


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: 963
Number of extensions: 57
Number of successful extensions: 6
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: 573
Length adjustment: 37
Effective length of query: 571
Effective length of database: 536
Effective search space:   306056
Effective search space used:   306056
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