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.

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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