GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Marinobacter adhaerens HP15

Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate GFF3421 HP15_3363 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__Marino:GFF3421
          Length = 562

 Score =  325 bits (832), Expect = 4e-93
 Identities = 204/549 (37%), Positives = 309/549 (56%), Gaps = 27/549 (4%)

Query: 28  RGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPVF 87
           R  L+  G+  + F  +P IGI +TWS++TPCN H+ +LAE+  AG  EAGG  L     
Sbjct: 27  RAMLRAVGFTDEDFK-KPQIGIASTWSNLTPCNMHINQLAEESAAGADEAGGKSLIFNTI 85

Query: 88  SASENTFRPT-----AMMYRNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCD 142
           + S+     T     +++ R + A ++E     +  DG V + GCDK  P  +MG A  +
Sbjct: 86  TISDGIANGTEGMKYSLVSREVIADSIETVAGCEGFDGLVAIGGCDKNMPGCMMGLARLN 145

Query: 143 LPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKA---GEMTQAEFLEAEASMSRSSGT 199
            PS+ V GG ++ G        + T +    E V A   G++   E  + E +     G+
Sbjct: 146 RPSVFVYGGTIMPGE-------NHTDIISVFEAVGAHARGDLDLIEVKQIEETAIPGPGS 198

Query: 200 CNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMT 259
           C  M TA+TMAS  EA+GM+L G++A   V   +    +  G  ++ +++ D+KPS+IMT
Sbjct: 199 CGGMYTANTMASAIEAMGMSLPGSSAQNAVSETKAEDCRGAGAAVLNLLEKDIKPSDIMT 258

Query: 260 KQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYL 319
           ++AFENAI    A+GGSTNAV+HLLA+A  VG+DL L+D+   G+ VP + +L PSG Y+
Sbjct: 259 RKAFENAITVVIALGGSTNAVLHLLAMASTVGVDLELEDFVEIGKRVPVLADLRPSGHYM 318

Query: 320 MEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNE--DVILPAEKALT 377
           M E    GG+  ++K L + GLLH D LTV+G+T+ + + DV  + E  D+I   +  + 
Sbjct: 319 MSELVAIGGIQPLMKMLLDRGLLHGDCLTVTGQTLAENLADVDPYPEGQDIIHAFDNPIK 378

Query: 378 SSGGIVVLRGNLAPKGAVLK-PSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLDIDENC 436
           +   + +L GNLAP GAV K       H     GRA VF   ++ + +I D  +   +  
Sbjct: 379 ADSHLRILFGNLAPTGAVAKITGKEGTHF---TGRARVFHSEEEAQERILDGTVVAGD-- 433

Query: 437 IMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGI-LDMVRISDARMSGTAYGTVVLHTSPEA 495
           ++V++  GPKG PGM E+  +     ++ KG+  D+  I+D R SG ++G VV H +PEA
Sbjct: 434 VLVIRYEGPKGGPGMREM--LSPTSAIMGKGLGSDVALITDGRFSGGSHGFVVGHITPEA 491

Query: 496 AVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYAFLHQQHVE 555
           A GGP+A+V++GD I +D  + R+ LD+SD+EL RR   WQ      T G    + + V 
Sbjct: 492 AEGGPIALVEDGDTITIDAVSNRIELDVSDQELERRRQAWQAPPPRFTRGTLAKYSRTVS 551

Query: 556 GADTGADLD 564
            A  GA  D
Sbjct: 552 SASKGAVTD 560


Lambda     K      H
   0.318    0.135    0.408 

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: 860
Number of extensions: 46
Number of successful extensions: 6
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: 579
Length of database: 562
Length adjustment: 36
Effective length of query: 543
Effective length of database: 526
Effective search space:   285618
Effective search space used:   285618
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.

Links

Downloads

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:

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