GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Pedobacter arcticus A12

Align Probable phosphoribomutase; PRM; Phosphoglucomutase 3 homolog; PGM 3 homolog; EC 5.4.2.7 (characterized)
to candidate WP_017257613.1 B176_RS0104620 phospho-sugar mutase

Query= SwissProt::O74478
         (587 letters)



>NCBI__GCF_000302595.1:WP_017257613.1
          Length = 578

 Score =  298 bits (763), Expect = 4e-85
 Identities = 190/554 (34%), Positives = 294/554 (53%), Gaps = 16/554 (2%)

Query: 1   MDPILQELVDEWFKLDQDETTRNEVSQLIKAEDYATLKQIMHPRIGFGTSGLRAEIGAGF 60
           +D   Q+ V++W   + DE T+ E+  L+ +     L    +  + FGT GLR  +GAG 
Sbjct: 4   LDKATQDRVNQWLNGNYDEATKAEIKALVDSNAVTELTDSFYKSLEFGTGGLRGIMGAGS 63

Query: 61  ARMNCLTVIQASQGFAEYLLQTVPSAAKLGVVIGHDHRHKSNTFARLTAAVFLQKGFKTY 120
            R+N  T+  A+QG A YL+   P   K+ V I HD R+ S+   ++TA VF   G   Y
Sbjct: 64  NRVNKYTIGAATQGLANYLINKYPGE-KIKVAIAHDSRNNSDVLGKITADVFSANGIHVY 122

Query: 121 FFDHLVHTPLVPFAVKTLGTAAGVMITASHNPAAYNGYKVYWGNGCAIIPPHDKGIAACI 180
           FF  L  TP + FAV+TLG  +GVM+TASHNP  YNGYK Y  +G   + P D+ +   +
Sbjct: 123 FFKALRPTPELSFAVRTLGCKSGVMLTASHNPKEYNGYKAYGEDGGQFVAPDDQLVMDEV 182

Query: 181 EK--NLTPITWDKNLVENHKLADRDFAVGLLKNYWSQLHEFHSENNFSLEMKSLKFVYTP 238
            K  ++  I +D    EN      +    + ++Y +++       +     K LK V++P
Sbjct: 183 AKVESVDDIKFDAK-PENISYIGEE----MDEDYLNKITSLSVSPDAIKRQKDLKIVFSP 237

Query: 239 IHGVGLPFVTSALHLFGEQGDMISVPLQDSPNPDFPTVKFPNPEEEGALDLAYEQADANG 298
           IHG G+  V +AL  FG + ++I V  Q +P+ DFPTV +PNPEE+ AL LA ++A    
Sbjct: 238 IHGTGITLVPAALKRFGFE-NVILVEEQTTPDGDFPTVVYPNPEEKEALTLALKKAKETD 296

Query: 299 ISYVLATDPDADRFAFAEK-INGAWRRFTGDEVGCILAYFIFQEYKNVGKPIDDFYVLST 357
              V+ATDPDADR   A K + G +    G++ G +L  ++ + ++  GK     YV+ T
Sbjct: 297 ADLVMATDPDADRVGIAVKNLKGEFELLNGNQTGSLLINYMLEAWEKEGKFTGKEYVIKT 356

Query: 358 TVSSAMVKSMAKVEGFHHVETLTGFKWLGNKALELEKQGKFIGLAYEEALGYMVGSIVRD 417
            V+S ++  +A  +      TLTGFK++G    ELE +  FI +  EE+ GY+VG  VRD
Sbjct: 357 IVTSYLIDKIAADKKVKCYNTLTGFKFIGQIMTELEGKETFI-VGGEESYGYLVGDFVRD 415

Query: 418 KDGVNALITFLHLLKRLQLQNLSITEVFEQMSKKYGYYTTQNSYFLSRDTPKLRALVDAL 477
           KD V +      +    + Q  S+ E    M  KYG+Y  +      +       +V  +
Sbjct: 416 KDAVVSAAFIAEMTAFYKDQGSSLYEAMINMYVKYGFYKEKLVSITKKGKSGAEEIVAMM 475

Query: 478 RHYDTKSGYPATLGSKKITNVRDLTTGYDSSSTDGKAT-LPVSKSSDNVTFELENGEVIM 536
             +  ++  P +LG  K+  ++D     +++  D   + +P+ K SD + F  E+G  I+
Sbjct: 476 ERF--RNNPPKSLGGSKVVTLKDYGQRKETNLVDNTTSEIPLPK-SDVLQFITEDG-CII 531

Query: 537 TIRTSGTEPKLKFY 550
           + R SGTEPK+KFY
Sbjct: 532 SARPSGTEPKIKFY 545


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: 819
Number of extensions: 51
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: 578
Length adjustment: 36
Effective length of query: 551
Effective length of database: 542
Effective search space:   298642
Effective search space used:   298642
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 24 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