GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deoB in Desulfovibrio vulgaris Miyazaki F

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate 8499281 DvMF_0059 phosphoglucosamine mutase (RefSeq)

Query= BRENDA::Q6I7B6
         (450 letters)



>lcl|FitnessBrowser__Miya:8499281 DvMF_0059 phosphoglucosamine
           mutase (RefSeq)
          Length = 450

 Score =  171 bits (432), Expect = 6e-47
 Identities = 140/465 (30%), Positives = 235/465 (50%), Gaps = 45/465 (9%)

Query: 2   RLFGTAGIRGTL-WEKVTPELAMKVGMAVGTY-----KSGKALVGRDGRTSSVMLKNAMI 55
           RLFGT G+RG +    +T ++A+++G+A GT+     +  + ++G+D R S  + ++A+ 
Sbjct: 4   RLFGTDGLRGQVNIYPMTADVALRLGLAAGTHFRNGNRRHRVVIGKDTRLSGYVFESALT 63

Query: 56  SGLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFYV 114
           +GL + GM+V     +PTPA+A+ TR + AD GV+I+ASHNP  DNG+K F+ DG +   
Sbjct: 64  AGLCAAGMDVYLVGPLPTPAIAFLTRNMRADLGVVISASHNPFMDNGIKFFDKDGFKLPD 123

Query: 115 EQERGLEEIIFSGNFRKARWDEIKPVR-----NVEVIPDYINAVL--DFVGHET--NLKV 165
           E E  + +++   ++   +WD   P R      +E  P      L   F  H T   ++V
Sbjct: 124 EMENKITDMVLDPDW---QWDYPAPERVGRAAKIEDSPGRYIVYLKNSFPAHLTLDGMRV 180

Query: 166 LYDGANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVD 225
           + D ANGA   VAP  L E+GA+V+ +    +G     +    Y  +A  GK V E   D
Sbjct: 181 VLDCANGANYKVAPLALEELGAEVIKIGTEPNGLNINHQCGSLYPGVA-AGK-VLETRAD 238

Query: 226 LAIAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHG--GGTVVVSIDTGSRIDAVV 283
           + +A DGDADR+ V DEKG  +D D ++AL A   +        T+V ++ +   ++  +
Sbjct: 239 VGLALDGDADRLIVVDEKGTVLDGDQIMALCADDMLRRGALRNNTLVATVMSNMALEVYM 298

Query: 284 ERAGGRVVRIPLGQPH--DGIKRYKAIFAAE-PWKLVHPKFGPWIDPFVTMGLLIKLIDE 340
           +  G +++R P+G  +  + ++R  A    E    L+    G   D  +    +++++ E
Sbjct: 299 KERGCKLLRTPVGDRYVVEAMRREGANLGGEQSGHLIFMDHGTTGDGLMAALQILRIMRE 358

Query: 341 -NGPLSELVKEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSE-IKEVLT-ISGFR 397
            + PLSEL  ++  +  +  NV                 VERK+  E  + VL  ++   
Sbjct: 359 RDRPLSELAGQLQLFPQELINV----------------HVERKIPFEQCQPVLDGVAKVE 402

Query: 398 IALNDGSWILIRPSGTEPKIRVVAEAPTEKRRDELFEMAYSTVSR 442
             L D   +L+R SGTE   RV+ E    ++   L  +   TV +
Sbjct: 403 AELGDRGRVLLRYSGTEAVCRVMVEGEDPEQVKRLASLLAETVQK 447


Lambda     K      H
   0.318    0.138    0.402 

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: 489
Number of extensions: 30
Number of successful extensions: 7
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: 450
Length of database: 450
Length adjustment: 33
Effective length of query: 417
Effective length of database: 417
Effective search space:   173889
Effective search space used:   173889
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 (21.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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