GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Echinicola vietnamensis KMM 6221, DSM 17526

Align Probable phosphoribomutase; PRM; Phosphoglucomutase 3 homolog; PGM 3 homolog; EC 5.4.2.7 (characterized)
to candidate Echvi_2982 Echvi_2982 Phosphomannomutase

Query= SwissProt::O74478
         (587 letters)



>FitnessBrowser__Cola:Echvi_2982
          Length = 575

 Score =  283 bits (724), Expect = 1e-80
 Identities = 181/558 (32%), Positives = 290/558 (51%), Gaps = 23/558 (4%)

Query: 12  WFKLDQDETTRNEVSQLIKAEDYATLKQIMHPRIGFGTSGLRAEIGAGFARMNCLTVIQA 71
           W   + D+ ++ ++ QL+ A D + L    +  + FGT GLR  +G G  RMN  TV  A
Sbjct: 13  WLNSNIDQESKTKIQQLLDASDSSELVDAFYKDLEFGTGGLRGVMGIGSNRMNVYTVGMA 72

Query: 72  SQGFAEYLLQTVPSAAKLGVVIGHDHRHKSNTFARLTAAVFLQKGFKTYFFDHLVHTPLV 131
           +QG A YLL   P    + V I HD R  +  FA  TA V    G K  +F+ +  TP++
Sbjct: 73  TQGLANYLLACFPGE-DIKVAITHDSRINNTLFAETTANVLTANGIKVKYFEEMRPTPML 131

Query: 132 PFAVKTLGTAAGVMITASHNPAAYNGYKVYWGNGCAIIPPHDKGIAACIE--KNLTPITW 189
            +A++  G  +GVMITASHNP  YNGYK YW +G  I+ PHDK I   ++  K++  + W
Sbjct: 132 SYAIRHYGCKSGVMITASHNPKEYNGYKAYWEDGGQIVAPHDKNIIMEVQKIKSIDDVKW 191

Query: 190 DKN--LVENHKLADRDFAVGLLKNYWSQLHEFHSENNFSLEMKSLKFVYTPIHGVGLPFV 247
           DKN  L+E +  A+ D        Y + + +F       L  + +  V++PIHG     V
Sbjct: 192 DKNDALIE-YIGAEMDL------TYLNDIKKFSLSPKAILNQRDMCIVFSPIHGASGKMV 244

Query: 248 TSALHLFGEQGDMISVPLQDSPNPDFPTVKFPNPEEEGALDLAYEQADANGISYVLATDP 307
            +AL  FG +   + V  Q++P+  FPTV +PNPEE  AL L+ + A       VLA DP
Sbjct: 245 PAALKTFGFENIHV-VKEQEAPDGTFPTVVYPNPEEAEALSLSLKLAKEVNAELVLACDP 303

Query: 308 DADRFAFA-EKINGAWRRFTGDEVGCILAYFIFQEYKNVGKPIDDFYVLSTTVSSAMVKS 366
           D DR+A A     G +    G++ G IL Y++  +++  G    D ++++T V++ +++ 
Sbjct: 304 DGDRYAAAIPNEKGEYELLNGNQTGSILTYYLLNQWREHGLFTGDQFMVNTIVTTELIEE 363

Query: 367 MAKVEGFHHVETLTGFKWLGNKALELEKQGKFIGLAYEEALGYMVGSIVRDKDGVNALIT 426
           +           LTGFK +     ELE + +F+G   EE+ G++VG  VRDKDGV+A   
Sbjct: 364 ICHGFNIPCYRVLTGFKNIAAIIRELEGKKQFVG-GGEESYGFLVGDAVRDKDGVSACAM 422

Query: 427 FLHLLKRLQLQNLSITEVFEQMSKKYGYYTTQNSYFLSRDTPKLRALVDALRHYDTKSGY 486
              ++   + + +++ +V  ++ + YG+Y  ++   +++        +  L H   ++  
Sbjct: 423 LAEVVAYYKEKGMTLFDVLAEIYQSYGFY-KESLISVTKKGKDGAEQIQQLMH-GFRTNR 480

Query: 487 PATLGSKKITNVRDLTTGYDSSSTDGKATLPVSKSSDNVTFELENGEVIMTIRTSGTEPK 546
           P  +   K+  V D+      +  DG         S+ + F LE+G  I + R SGTEPK
Sbjct: 481 PEAINGTKVVKVVDVKESKVYNIADGTEEDLDLDKSNVIQFYLEDGSKI-SARPSGTEPK 539

Query: 547 LKFYICARGHSLEDSIKN 564
           +K+YI     S+ +S+ N
Sbjct: 540 IKYYI-----SVNESLPN 552


Lambda     K      H
   0.318    0.135    0.401 

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: 830
Number of extensions: 42
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: 587
Length of database: 575
Length adjustment: 36
Effective length of query: 551
Effective length of database: 539
Effective search space:   296989
Effective search space used:   296989
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.

Links

Downloads

Related tools

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