GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Korea:Ga0059261_4216 Ga0059261_4216
           Dihydroxyacid dehydratase/phosphogluconate dehydratase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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