GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pgmA in Desulfovibrio vulgaris Miyazaki F

Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate 8501959 DvMF_2673 Phosphomannomutase (RefSeq)

Query= BRENDA::P26276
         (463 letters)



>lcl|FitnessBrowser__Miya:8501959 DvMF_2673 Phosphomannomutase
           (RefSeq)
          Length = 464

 Score =  395 bits (1016), Expect = e-114
 Identities = 206/445 (46%), Positives = 273/445 (61%), Gaps = 6/445 (1%)

Query: 14  FRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQLIQGLV 73
           FRAYDIRG+V     AE    +GRA G+  L RG     VG D R S P     L  GL+
Sbjct: 9   FRAYDIRGIVDADFDAEWVERLGRACGTYLLERGIGAAVVGHDCRHSSPAYHDALTAGLI 68

Query: 74  DCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGETLANEQIQA 133
            CG  V  VGMVPTP+LY+A   LE + G+M+T SHNPP+YNGFK+     T+   +I+ 
Sbjct: 69  ACGIDVVSVGMVPTPLLYFAVRHLERQGGIMITASHNPPEYNGFKVWAGQTTIHTTEIRR 128

Query: 134 LRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAK----PMKVVVDCGNGVAGVIAP 189
           + E       ASG G    +DI+P Y + +   + +A     P+KVVVD GNG  G I  
Sbjct: 129 IYEIFAAGRFASGKGVGCTMDIVPAYMEAVTQRVQLAPRARGPLKVVVDGGNGAGGDICA 188

Query: 190 QLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGDRVG 249
            L+  LG  VI  YC+ DG FPNHHPDP    N++DLIA+V +E ADLG+  DGD DR+G
Sbjct: 189 DLLRRLGADVIEQYCDPDGAFPNHHPDPVVEANMRDLIARVASEGADLGIGLDGDADRLG 248

Query: 250 VVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKTGHS 309
            V   G +++ D LL LFA+D+++R PG +++ DVKC+ RL   I  +GG+P MW TGHS
Sbjct: 249 AVDAQGRLLFGDELLSLFARDLLARVPGGEVMADVKCSHRLFRDIEAHGGKPTMWITGHS 308

Query: 310 LIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFSAFPS 369
           ++K +M E  A LAGEMSGH+FF E W+GFDD IY+AA LL ILS            +P 
Sbjct: 309 VMKARMLEVNAPLAGEMSGHMFFNEGWYGFDDAIYAAALLLRILSASDVPLT-ALPGWPP 367

Query: 370 DISTPEINITVTEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLVRASNTTPVL 429
             +TPE+++   ++ KFA++   Q   +    ++  +DG R+ +P GW LVRASNT PVL
Sbjct: 368 SHATPELHMPCPDELKFAVVSRAQEHFR-ALYDVNEIDGARITWPDGWALVRASNTQPVL 426

Query: 430 VLRFEADTEEELERIKTVFRNQLKA 454
           VLRFEA+T E L  I+T+    L A
Sbjct: 427 VLRFEAETPERLAEIRTLVETPLAA 451


Lambda     K      H
   0.319    0.138    0.410 

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: 588
Number of extensions: 27
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: 463
Length of database: 464
Length adjustment: 33
Effective length of query: 430
Effective length of database: 431
Effective search space:   185330
Effective search space used:   185330
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 (21.7 bits)
S2: 51 (24.3 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 preprint 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