Alignments for a candidate for edd in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Shewanella loihica PV-4

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate 5207771 Shew_0292 dihydroxy-acid dehydratase (RefSeq)

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__PV4:5207771
          Length = 616

 Score =  208 bits (529), Expect = 6e-58
 Identities = 182/584 (31%), Positives = 268/584 (45%), Gaps = 49/584 (8%)

Query: 68  VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127
           VAI +S+   +  H   +     +  A+ E G + +    T A+ DG+  G  GM  SLP
Sbjct: 37  VAIANSFTQFVPGHVHLKDMGSLVAGAIEEAGGIAK-EFNTIAVDDGIAMGHGGMLYSLP 95

Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG--- 184
           SRE+IA S    ++ +  DA + +  CDKI PG++M ALR  ++P +FV GGPM +G   
Sbjct: 96  SRELIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRL-NIPVVFVSGGPMEAGKTK 154

Query: 185 ISNK----EKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           +S+K    +  D     A+ + + E+  + E  +  + G+C+   TAN+   L E +GL 
Sbjct: 155 LSDKLIKLDLVDAMVAAADDRVSDEDSEKIERSACPTCGSCSGMFTANSMNCLTEALGLS 214

Query: 241 LPGASFVNPYTPLRDALTHEAAQQV----TRLTKQSGNFTPIGEIVDERSLVNSIVALHA 296
           LPG   +      R  L  EA ++V     R  +          I   ++  N++    A
Sbjct: 215 LPGNGSLLATHSDRRELFLEAGRRVMALANRYYRDDDESALPRNIASFKAFENAMALDIA 274

Query: 297 TGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN-GKADINHFQAAGGMAF 355
            GGS+N  LH+ A AQ A +  T  D+  LS  VP L  V P+  K  +     AGG+  
Sbjct: 275 MGGSSNTVLHLLAAAQEAKVDFTMADIDRLSRQVPHLCKVAPSTPKYHMEDVHRAGGVMG 334

Query: 356 LIRELLEAGLLHEDVNTVAGRGLS----RYTQEPFLDNG-KLVWRDGPI----------- 399
           ++ EL  AGLLH DV+ VAG  L     +Y      D   +  +  GP            
Sbjct: 335 ILGELDRAGLLHTDVSHVAGENLKAVLVQYDLVQTQDEAVQQFYAAGPAGIPTTKAFSQS 394

Query: 400 ---ESLD----ENILRPVARAFSPEGGLRVMEGNLGRG--VMKVSAVALQHQIVEAPAVV 450
               SLD    E  +R    AFS EGGL V+ GN+     ++K + V   +      A V
Sbjct: 395 CRWPSLDVDRQEGCIRTREFAFSQEGGLAVLSGNIAADGCIVKTAGVDEANHTFVGHARV 454

Query: 451 FQDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTD 509
           ++ Q D       GE+    V V+R++GP+   GM E+   T +L   +  G   AL+TD
Sbjct: 455 YESQDDAVAGILGGEVVAGDVVVIRYEGPKGGPGMQEMLYPTSYL-KSKGLGTSCALITD 513

Query: 510 GRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAAREPAK 569
           GR SG +  +    HVSPEA  GG +A V  GD I +D    ++ L V  +    R  A 
Sbjct: 514 GRFSGGTSGLSIG-HVSPEAAAGGTIALVETGDRIEIDIPARSITLAVSDEVLETRRQAM 572

Query: 570 GLLG-------NNVGSGRELFGFMRMAFSSAEQGASAFTSALEN 606
              G       N   S         M  +SA++GA    S LE+
Sbjct: 573 QARGKQAWKPVNRERSVSLALKAYAMLATSADKGAVRDVSKLED 616


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: 894
Number of extensions: 54
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 608
Length of database: 616
Length adjustment: 37
Effective length of query: 571
Effective length of database: 579
Effective search space:   330609
Effective search space used:   330609
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 paper from 2022 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

GapMind for catabolism of small carbon sources