GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Methanococcus aeolicus Nankai-3

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_011973396.1 MAEO_RS03385 dihydroxy-acid dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_000017185.1:WP_011973396.1
          Length = 550

 Score =  244 bits (623), Expect = 7e-69
 Identities = 173/545 (31%), Positives = 278/545 (51%), Gaps = 41/545 (7%)

Query: 32  SDGPQRGKLQCANFAHGVAGCGSEDKHSLRMMNAANVAIVSSYNDMLSAHQPYEHFPEQI 91
           SD  ++G  +  N +  +  CG  D+     +    + IV+S+ +++  H       E  
Sbjct: 3   SDNLKKGVSRAPNRSL-LKACGYTDEE----IEKPFIGIVNSFTEVVPGHIHLNTLAEAA 57

Query: 92  KKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLPSREVIALSTAVALSHNMFDAALML 151
           KK +   G    F   T A+CDG+  G  GM  SLPSRE+IA +       + FD  +++
Sbjct: 58  KKGVYANGGT-PFEFNTMAVCDGIAMGHEGMRYSLPSREIIADTVESMAKAHGFDGLVLI 116

Query: 152 GICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGISNKEKADVRQ------RYAEGKATRE 205
             CDKIVPG++MGALR  ++P I + GGPM  G  + +K D+         Y  GK T+E
Sbjct: 117 PSCDKIVPGMIMGALRL-NIPFIVITGGPMQPGELHGKKYDLISVFEGVGEYNVGKITKE 175

Query: 206 ELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLPGASFVNPYTPLRDALTHEAAQQV 265
           EL+E E  +    G+C    TAN+   L E +GL LP  +  +     +  +   +  ++
Sbjct: 176 ELMEIETCACPGAGSCAGLFTANSMACLTETLGLSLPMCATTHATDAEKVRIAKRSGMKI 235

Query: 266 TRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGSTNHTLHMPAIA-QAAGIQLTWQDMA 324
             L K+    T   +++ + S  N+I+   A GGS+N TLH+PA+A + A   +T  D  
Sbjct: 236 VDLVKEDIKPT---DLLTKESFENAILVDLALGGSSNTTLHIPALAYEIAPEFITLDDFD 292

Query: 325 DLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELLEAGLLHEDVNTVAGRGLSRYTQE 384
            L + VP ++ + P G   I+    AGG+  +++ +LE  +   D NTV+G+ +     E
Sbjct: 293 RLCDEVPHIASLRPGGDHFISDLHRAGGIPAVLK-ILEQKI--RDANTVSGKSIKEIINE 349

Query: 385 PFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGLRVMEGNLGRG--VMKVSAVALQHQ 442
                         ++ +D NI+RPV +      GLR+++GN+     V+K+SAV  +  
Sbjct: 350 --------------VKYIDYNIIRPVDKPVHETAGLRILKGNIAPDGCVVKISAVNPKMY 395

Query: 443 IVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSNGMPELHKMTPFLGVLQDRGF 502
             E PA VF  +++  DA   G++++  V V+R++GP   G P + +M      +   G 
Sbjct: 396 KHEGPARVFNSEEETIDAILGGDIKEGDVVVIRYEGPA--GGPGMREMLSPTSAICGMGL 453

Query: 503 --KVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDAD 560
              VAL+TDGR SG S + P   H+SPEA  GG +A + +GDII +D +   + LK+  +
Sbjct: 454 DDSVALITDGRFSGGS-RGPCIGHISPEAMAGGPIAIIEEGDIIAIDMMAKEINLKISEE 512

Query: 561 EFAAR 565
           E   R
Sbjct: 513 EIKER 517


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: 853
Number of extensions: 55
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: 608
Length of database: 550
Length adjustment: 36
Effective length of query: 572
Effective length of database: 514
Effective search space:   294008
Effective search space used:   294008
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 Apr 09 2024. 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