GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gci in Phaeobacter inhibens BS107

Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate GFF443 PGA1_c04540 putative d-galactonate dehydratase

Query= BRENDA::A9CEQ8
         (378 letters)



>FitnessBrowser__Phaeo:GFF443
          Length = 410

 Score =  146 bits (368), Expect = 1e-39
 Identities = 109/363 (30%), Positives = 168/363 (46%), Gaps = 34/363 (9%)

Query: 29  RAHVLVEIECDDGTVGWGEC----LGPARPNAAVVQAYSGWLIGQDPRQTEKIWAVLYNA 84
           R  +LV++  D G  GWGEC    +GP      +   +   + G +P   E ++   Y++
Sbjct: 21  RYWILVKVTTDTGITGWGECYAASVGPDAMTHVIRDVFERHMQGMNPENIEWMFRRAYSS 80

Query: 85  LRDQGQRGLSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRAYA-TGSFKRDNVD 143
              Q      + A SG++IA WDI GK     +  L+GGR  + +RAY         ++D
Sbjct: 81  GFTQRPDLSVMGAFSGLEIACWDILGKDRDRPVHALIGGRMNDRLRAYTYLYPLPHHDID 140

Query: 144 RVSDNASEMAERRA-----EGFHACK-------------IKIGFGVEEDLRVIAAVREAI 185
               N  E+A   A     +G+ A K             +     + + +    A+REA+
Sbjct: 141 AFW-NTPELAAESAIAAVEKGYTAVKFDPAGPYTMRGGHMPAQSDITQSVAFCRAIREAV 199

Query: 186 GPDMRLMIDANHGYTVTEAITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQPIPVAGG 245
           G    L+   +  +T   AI LG     +   WFEEP  P+ +   ARV     IPVA G
Sbjct: 200 GDRADLLFGTHGQFTPAGAIRLGQALESYEPLWFEEPTPPDLVADMARVADRVRIPVATG 259

Query: 246 ETWHGRYGMWQALSAGAVDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIA 305
           E    +      L AGA +ILQP L   GG  E +KIA +A + G ++ PH++   V+ A
Sbjct: 260 ERLTTKAEFAAILRAGAAEILQPALGRSGGIWETKKIAAIAEVFGAQMAPHLYAGPVEWA 319

Query: 306 AALQFMAAMTPDPVRVNPIEPIMEFDRTHNPFRQAVLREPLEAVNGVVTIPDGPGLGIEI 365
           A +Q +AA  P+ + +  IE          PF  A++++ +   +G V   D PGLGIE+
Sbjct: 320 ANIQ-LAASIPNLLMIETIE---------TPFHTALIKQGITVEDGFVIPSDTPGLGIEV 369

Query: 366 NRD 368
           + D
Sbjct: 370 DED 372


Lambda     K      H
   0.321    0.138    0.431 

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: 487
Number of extensions: 31
Number of successful extensions: 4
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: 378
Length of database: 410
Length adjustment: 31
Effective length of query: 347
Effective length of database: 379
Effective search space:   131513
Effective search space used:   131513
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 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