GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Phaeobacter inhibens BS107

Align phosphogluconate dehydratase (characterized)
to candidate GFF2902 PGA1_c29490 dihydroxy-acid dehydratase LivD

Query= CharProtDB::CH_024239
         (603 letters)



>FitnessBrowser__Phaeo:GFF2902
          Length = 614

 Score =  182 bits (463), Expect = 3e-50
 Identities = 156/538 (28%), Positives = 251/538 (46%), Gaps = 45/538 (8%)

Query: 68  IAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQDGMELSLL 127
           IAI+ S+   +  H   +   +++ + +  A  V +    + A+ DG+  G DGM  SL 
Sbjct: 37  IAIVNSFTQFVPGHVHLKDLGQMVAREVEAAGGVAKEFNTI-AVDDGIAMGHDGMLYSLP 95

Query: 128 SREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGL-- 185
           SREVIA S    ++ +  D  + +  CDKI PG+ MAA+   ++PA+FV  GPM +G   
Sbjct: 96  SREVIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRL-NIPAIFVSGGPMEAGKID 154

Query: 186 ---PNKEKVRIRQLYAEGKVDRMA---LLESEAASYHAPGTCTFYGTANTNQMVVEFMGM 239
               + +K+ +         D M    +   E  +    G+C+   TAN+   + E +G+
Sbjct: 155 IADLDMKKIDLVDAMVAAASDTMTDEQVQHIEENACPTCGSCSGMFTANSMNCLAEALGL 214

Query: 240 QLPGSSFVHPDSPLRDALTAAAARQVTRMTGN---GNEWMPIGKMIDEKVVVNGIVAL-L 295
            LPG+         R  L   A R++  +T     G E   + + I         ++L +
Sbjct: 215 ALPGNGSTLATHADRKHLFLEAGRKIVDITKRHYVGEEKGLLPREIATFDAFENAMSLDI 274

Query: 296 ATGGSTNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPN-GPADINHFQAAGGVP 354
           A GGSTN  +HL+A+A    +     D   LS  VP + ++ PN     +     AGG+ 
Sbjct: 275 AMGGSTNTVLHLLAIANEGKVDFTMTDMDRLSRKVPCLCKVAPNIENVHMEDVHRAGGIF 334

Query: 355 VLVRELLKAGLLHEDVNTV----AGFGLSRYTLEPWLN---------------NGELDWR 395
            ++ EL +AGLLH + +TV     G  ++++ ++   N                 E   +
Sbjct: 335 SILGELSRAGLLHNECSTVHSSTMGEAIAKWDIKVANNPDAEALFKAAPGGVRTTEAFSQ 394

Query: 396 EGAEKSLDSN----VIASFEQPFSHHGGTKVLSGNLGR--AVMKTSAVPVENQVIEAPAV 449
               K LD++    VI S +  FS  GG  VL GN+ R   ++KT+ V          A 
Sbjct: 395 SNRYKELDTDREGGVIRSKDHAFSQDGGLAVLFGNIARDGCIVKTAGVDDNILKFTGSAY 454

Query: 450 VFESQHDVMPAFEAGLLDRDCVVVVRHQGPKANGMPELHKLMPPLGVLLDRCF--KIALV 507
           V ESQ   +       +    VVV+R++GP+  G P + +++ P   L  +      AL+
Sbjct: 455 VCESQDQAVNDILTSKVKEGDVVVIRYEGPR--GGPGMQEMLYPTSYLKSKGLGKACALL 512

Query: 508 TDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRDGDIIRVNGQTGELTLLVDEAELAAR 565
           TDGR SG +  + S  HV+PEA +GG +  V+ GD I ++     + L V + ELAAR
Sbjct: 513 TDGRFSGGTSGL-SIGHVSPEAAEGGTIGLVQQGDTIEIDIPNRTIHLAVSDEELAAR 569


Lambda     K      H
   0.318    0.134    0.392 

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: 877
Number of extensions: 53
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: 603
Length of database: 614
Length adjustment: 37
Effective length of query: 566
Effective length of database: 577
Effective search space:   326582
Effective search space used:   326582
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