GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Marino:GFF3421 HP15_3363 dihydroxy-acid
           dehydratase
          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.

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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 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