Alignments for a candidate for edd in Jannaschia aquimarina GSW-M26

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Jannaschia aquimarina GSW-M26

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_043918762.1 jaqu_RS09665 dihydroxy-acid dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_000877395.1:WP_043918762.1
          Length = 587

 Score =  219 bits (559), Expect = 2e-61
 Identities = 170/556 (30%), Positives = 267/556 (48%), Gaps = 52/556 (9%)

Query: 32  SDGPQRGKLQCANFAHGVAGCGSEDKHSLRMMNAANVAIVSSYNDMLSAHQPYEHFPEQI 91
           ++GP R   +   +A G+   G E+ H         V + + +N+    +       + +
Sbjct: 17  TEGPARAPHRSYFYAMGL---GDEEIHQ------PFVGVATCWNEAAPCNIALNRQAQAV 67

Query: 92  KKALREM-GSVGQFAGGTPAMCDGVTQGEAGMELSLPSREVIALSTAVALSHNMFDAALM 150
           K  +++  G+  +F   T  + DG+  G  GM  SL SR+ IA +  + +  + +DA + 
Sbjct: 68  KLGVKQASGTPREFT--TITVTDGIAMGHEGMRSSLASRDAIADTVELTMRGHCYDALVG 125

Query: 151 LGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGISNKEKADVRQRYAEGKATREELLES 210
           L  CDK +PG+MM  +R  + P++F+ GG +  G +    A+V   Y     T +++ E+
Sbjct: 126 LAGCDKSLPGMMMAMVRL-NTPSVFIYGGSILPGKA-PAGANVPDEYKNRDLTVQDMFEA 183

Query: 211 -----------------EMKSYHSPGTCTFYGTANTNQLLMEVMGLHLPGASFVNPYTPL 253
                            E  +  S G C    TANT   + E +GL LP +S        
Sbjct: 184 VGNHQAGNLSDEALDVLERVACPSAGACGGQFTANTMACVSEAIGLALPNSSGAPAPYES 243

Query: 254 RDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGSTNHTLHMPAIAQA 313
           RD  +  + + V RL +++       +IV  +SL N+   +  TGGSTN  LH+PAIA  
Sbjct: 244 RDQYSIASGEAVMRLLEKN---IRARDIVTRKSLENAARVVACTGGSTNAGLHLPAIAHE 300

Query: 314 AGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELLEAGLLHEDVNTV 373
           AGI     D+ ++    P    + P G+        AGG+  +++EL +AGL+HED  T 
Sbjct: 301 AGIDFDLFDVCEIFRDTPYFVDLKPGGQYVAKDLYEAGGVPVVMKELRKAGLIHEDCITA 360

Query: 374 AGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGLRVMEGNLG--RGV 431
            G+ +        LD  K           D  ++ PV    +P GG+  ++GNL     +
Sbjct: 361 TGKTIGE-----VLDEVK--------GEADGKVIYPVDAPITPTGGVVGLKGNLAPDGAI 407

Query: 432 MKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKM 490
           +KV+ +  QHQ    PA VF+ ++D   A KA   E+  V V+R +GP    GM E+   
Sbjct: 408 VKVAGIPSQHQRFTGPARVFECEEDAFAAVKARAYEEGEVLVIRNEGPAGGPGMREMLAT 467

Query: 491 TPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVK 550
           T  L   Q  G KVAL+TDGR SGA+       HV PEA  GG +  +RDGD+I +D +K
Sbjct: 468 TAALSG-QGMGKKVALITDGRFSGATRGFCVG-HVGPEAAHGGPIGMLRDGDVITIDAIK 525

Query: 551 GTLELKVDADEFAARE 566
           G L + +  +E  AR+
Sbjct: 526 GELSVDLTEEELVARK 541


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: 1014
Number of extensions: 66
Number of successful extensions: 7
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: 587
Length adjustment: 37
Effective length of query: 571
Effective length of database: 550
Effective search space:   314050
Effective search space used:   314050
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 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources