GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Pseudomonas stutzeri RCH2

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate GFF233 Psest_0234 dihydroxy-acid dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__psRCH2:GFF233
          Length = 612

 Score =  214 bits (545), Expect = 9e-60
 Identities = 166/534 (31%), Positives = 262/534 (49%), Gaps = 40/534 (7%)

Query: 68  VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127
           +AI +S+   +  H   +   + + + + + G V +    T A+ DG+  G  GM  SLP
Sbjct: 37  IAIANSFTQFVPGHVHLKDLGQLVAREIEKHGGVAK-EFNTIAVDDGIAMGHDGMLYSLP 95

Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGIS- 186
           SRE+IA S    ++ +  DA + +  CDKI PG++M ALR  ++P +FV GGPM +G + 
Sbjct: 96  SREIIADSVEYMVNAHCADAIVCISNCDKITPGMLMAALRL-NIPVVFVSGGPMEAGKTK 154

Query: 187 ----NKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLP 242
                 +  D     A+  A+ E++ E E  +  + G+C+   TAN+   L E +GL LP
Sbjct: 155 LASHGLDLVDAMVIAADESASDEKVAEYERSACPTCGSCSGMFTANSMNCLAEALGLALP 214

Query: 243 GASFVNPYTPLRDALTHEAAQQVTRLTKQ---SGNFTPI-GEIVDERSLVNSIVALHATG 298
           G          R+ L   A + V  L K+    G+ + +   I   R+  N++    A G
Sbjct: 215 GNGSTLATHSDREQLFLRAGRTVVELCKRYYGEGDESVLPRNIASRRAFENAMTLDIAMG 274

Query: 299 GSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN-GKADINHFQAAGGMAFLI 357
           GSTN  LH+ A AQ A +    + +  LS  VP L  V PN  K  +     AGG+  ++
Sbjct: 275 GSTNTILHLLAAAQEAEVDFDLRAIDALSRKVPQLCKVAPNIQKYHMEDVHRAGGIFSIL 334

Query: 358 RELLEAGLLHEDVNTVAGR----GLSRYTQEPFLDNG-KLVWRDGPI------------- 399
            EL   GLLH DV TV  R    G++++      D      ++ GP              
Sbjct: 335 GELARGGLLHTDVPTVHSRTLAEGIAQWDITQTQDEAVHTFFKAGPAGIPTQTAFSQSTR 394

Query: 400 -ESLDEN----ILRPVARAFSPEGGLRVMEGNLGRG--VMKVSAVALQHQIVEAPAVVFQ 452
            +SLD++     +R V  A+S EGGL V+ GN+     V+K + V     + E  A +++
Sbjct: 395 WDSLDDDRENGCIRSVEHAYSQEGGLAVLYGNIALDGCVVKTAGVDESIHVFEGTAKIYE 454

Query: 453 DQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTDGR 511
            Q        A E++   + ++R++GP+   GM E+   T +L   +  G   AL+TDGR
Sbjct: 455 SQDSAVKGILADEVKAGDIVIIRYEGPKGGPGMQEMLYPTSYL-KSKGLGKDCALLTDGR 513

Query: 512 MSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAAR 565
            SG +  +    H SPEA  GGA+  VRDGD + +D    +++L+V  +E + R
Sbjct: 514 FSGGTSGLSIG-HASPEAAAGGAIGLVRDGDKVLIDIPNRSIQLQVSDEELSHR 566


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: 871
Number of extensions: 58
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: 612
Length adjustment: 37
Effective length of query: 571
Effective length of database: 575
Effective search space:   328325
Effective search space used:   328325
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