GapMind for catabolism of small carbon sources

 

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

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate 353476 BT3950 phosphoglucomutase/phosphomannomutase (NCBI ptt file)

Query= metacyc::MONOMER-13382
         (455 letters)



>FitnessBrowser__Btheta:353476
          Length = 462

 Score =  254 bits (650), Expect = 3e-72
 Identities = 166/443 (37%), Positives = 241/443 (54%), Gaps = 13/443 (2%)

Query: 6   GTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKP-LVVVGRDTRVSGEMLKEALISG 64
           GT G  G A E + P   +K   A+ TL+++  + +   +VVGRD R+SGEM+K  ++  
Sbjct: 12  GTIG--GGAGEGLNPLDIVKFTSAYATLIRKTCKAQSNKIVVGRDARISGEMVKNVVVGT 69

Query: 65  LLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKER 124
           L+ +G DV+D+ +A TP  + A     A GG ++TASHNP ++N +KLL  +G  L  E 
Sbjct: 70  LMGMGWDVVDIDLASTPTTELAVTMEGACGGIILTASHNPKQWNALKLLNEHGEFLNAEE 129

Query: 125 EAIVEELFFKEDFDRAKWYEIGEVRRE-DIIKPYIEAIKS--KVDVEAIKKRKPFVVVDT 181
              V  +   E+FD A    +G  R++    + +I+++ +   VDVEAIKK    V +D 
Sbjct: 130 GNEVLRIAEAEEFDYADVDHLGSYRKDLTYNQKHIDSVLALDLVDVEAIKKANFRVAIDC 189

Query: 182 SNGAGSLTLPYLLRELGCK-VITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGV 240
            N  G + LP LL  LG K V  +  +P G F   NPEP E+NL + M ++K   AD   
Sbjct: 190 VNSVGGIILPELLERLGVKHVEKLYCEPTGNF-QHNPEPLEKNLGDIMNLMKGGKADVAF 248

Query: 241 AQDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKGGGLLVTTVATSNLLDDIAKKHGA 300
             D D DR   I ENG     + T   VAD VLK   G   V+ ++++  L D+ +K+G 
Sbjct: 249 VVDPDVDRLAMICENGVMYGEEYTLVTVADYVLKHTPGN-TVSNLSSTRALRDVTRKYGM 307

Query: 301 KVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSGKKF 360
           +   + VG++ V   +   N  IGGE NGGVI+P    GRD  + +A  +   A  GKK 
Sbjct: 308 EYSASAVGEVNVVTKMKATNAVIGGEGNGGVIYPASHYGRDALVGIALFLSHLAHEGKKV 367

Query: 361 SELIDELPKYYQIKTKRHV--EGDRHAIVNKVAEMARERGYTVDTTDGAKIIFEDGWVLV 418
           SEL    P Y+  K +  +  E D  AI+ KV E+ +     ++  DG KI F D WV +
Sbjct: 368 SELRATYPPYFIAKNRVDLIPEIDVDAILAKVKEIYKNE--EINDIDGVKIDFADKWVHL 425

Query: 419 RASGTEPIIRIFSEAKSKEKAQE 441
           R S TEPIIR++SEA +   A+E
Sbjct: 426 RKSNTEPIIRVYSEASTMGAAEE 448


Lambda     K      H
   0.317    0.138    0.391 

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: 494
Number of extensions: 31
Number of successful extensions: 5
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: 455
Length of database: 462
Length adjustment: 33
Effective length of query: 422
Effective length of database: 429
Effective search space:   181038
Effective search space used:   181038
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 (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