GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Bacteroides thetaiotaomicron VPI-5482

Align Phosphoglucomutase-2; PGM 2; Glucose phosphomutase 2; Phosphodeoxyribomutase; Phosphopentomutase; EC 5.4.2.2; EC 5.4.2.7 (characterized)
to candidate 351076 BT1548 phosphoglucomutase phosphomannomutase (NCBI ptt file)

Query= SwissProt::Q96G03
         (612 letters)



>FitnessBrowser__Btheta:351076
          Length = 581

 Score =  312 bits (799), Expect = 3e-89
 Identities = 194/566 (34%), Positives = 298/566 (52%), Gaps = 30/566 (5%)

Query: 14  RLDQETAQWLRWDKNSLTLEAVKRLIAEGNKEELRKCFGARMEFGTAGLRAAMGPGISRM 73
           ++ ++  +WL    ++ T   VKR++   +K EL + F   +EFGT GLR  MG G +RM
Sbjct: 9   QVTEKAEKWLTPAYDAETQAEVKRMLENEDKTELIEAFYKDLEFGTGGLRGIMGVGSNRM 68

Query: 74  NDLTIIQTTQGFCRYLEKQFSDLKQKGIVISFDARAHPSSGGSSRRFARLAATTFISQGI 133
           N  T+   TQG   YL+K F DL Q  +V+  D R       +SR FA  +A  F + GI
Sbjct: 69  NIYTVGAATQGLSNYLKKNFKDLPQISVVVGHDCR------NNSRLFAETSANIFSANGI 122

Query: 134 PVYLFSDITPTPFVPFTVSHLKLCAGIMITASHNPKQDNGYKVYWDNGAQIISPHDKGIS 193
            VYLF D+ PTP + F + HL   +GI++TASHNPK+ NGYK YWD+GAQ+++PHD GI 
Sbjct: 123 KVYLFDDMRPTPEMSFAIRHLGCQSGIILTASHNPKEYNGYKAYWDDGAQVLAPHDAGII 182

Query: 194 QAIEENLEPWPQAWDDSLIDSSPLLHNPSASINNDYFEDLKKYCFH-RSVNRETKVKFVH 252
             +         A D     +  L+      I+  Y + +K       ++ R   +K V+
Sbjct: 183 DEVNN----IASAADIKFKGNPDLIQIIGEDIDKIYLDMVKTVSIDPEAIARHKDMKIVY 238

Query: 253 TSVHGVGHSFVQSAFKAFDLVPPEAVPEQKDPDPEFPTVKYPNPEEGKGVLTLSFALADK 312
           T +HG G   +  A K +       VPEQ   D  FPTV  PNPE  +  L+++  LA +
Sbjct: 239 TPIHGTGMMLIPRALKMWGFENVFTVPEQMIKDGNFPTVISPNPENAE-ALSMAVNLAKE 297

Query: 313 TKARIVLANDPDADRLAVAEKQDSGEWRVFSGNELGALLGWWLFTSWKEKNQDRSALKDT 372
             A +V+A+DPDADR+ +A K D GEW + +GN+   +  +++ T +K+  + +    + 
Sbjct: 298 IDADLVMASDPDADRVGIACKDDKGEWVLINGNQTCMMYLYYILTQYKQLGKIKG---NE 354

Query: 373 YMLSSTVSSKILRAIALKEGFHFEETLTGFKWMGNRAKQLIDQGKTVLFAFEEAIGYMCC 432
           + + + V++++++ IA K      +  TGFKW+  R  +L +  K  +   EE+ G++  
Sbjct: 355 FCVKTIVTTELIKKIADKNNIEMLDCYTGFKWIA-REIRLREGKKKYIGGGEESYGFLAE 413

Query: 433 PFVLDKDGVSAAVISAELASFLATKNLSLSQQLKAIYVEYGY------HITKASYFICHD 486
            FV DKD VSA  + AE+A++      SL Q L  IYVEYG+      ++ K        
Sbjct: 414 DFVRDKDAVSACCLIAEVAAWAKDNGKSLYQLLLDIYVEYGFSKEFTVNVVKPGK---SG 470

Query: 487 QETIKKLFENLRNYDGKNNYPKACGKFEISAIRDLTTGYDDSQPDKKAVLPTSKSSQMIT 546
            E IK + EN R      N PK  G  ++   +D  T        K   L   ++S ++ 
Sbjct: 471 AEEIKAMMENFR-----ANPPKELGGSKVILSKDYKTLKQTDAEGKVTDLDMPETSNVLQ 525

Query: 547 FTFANGGVATMRTSGTEPKIKYYAEL 572
           +   +G   ++R SGTEPKIK+Y E+
Sbjct: 526 YFTEDGSKVSVRPSGTEPKIKFYMEV 551


Lambda     K      H
   0.317    0.133    0.399 

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: 881
Number of extensions: 41
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: 612
Length of database: 581
Length adjustment: 37
Effective length of query: 575
Effective length of database: 544
Effective search space:   312800
Effective search space used:   312800
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