GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Shewanella loihica PV-4

Align Probable phosphoribomutase; PRM; Phosphoglucomutase 3 homolog; PGM 3 homolog; EC 5.4.2.7 (characterized)
to candidate 5210100 Shew_2544 phosphoglucomutase/phosphomannomutase alpha/beta/subunit (RefSeq)

Query= SwissProt::O74478
         (587 letters)



>FitnessBrowser__PV4:5210100
          Length = 584

 Score =  325 bits (833), Expect = 3e-93
 Identities = 212/604 (35%), Positives = 308/604 (50%), Gaps = 43/604 (7%)

Query: 1   MDPILQELVDEWFKLDQDETTRNEVSQLIKAEDYATLKQIMHPRIGFGTSGLRAEIGAGF 60
           M   +Q  +  W  LD D  +R E+  L+       L      R+ FGT+G+R  +GAG 
Sbjct: 1   MQTQIQARIKHWLSLDSDAKSRAEIQALVDQGAQEELVARFAGRLTFGTAGIRGVVGAGP 60

Query: 61  ARMNCLTVIQASQGFAEYLLQTVPSAAKLGVVIGHDHRHKSNTFARLTAAVFLQKGFKTY 120
            RMN L V Q S+G AEYL   V +A   GVVIG+D RH S  FA   A+V    GFK +
Sbjct: 61  MRMNRLVVQQTSKGVAEYLKAQVENAVSRGVVIGYDGRHDSKQFAEDAASVLTAAGFKVF 120

Query: 121 FFDHLVHTPLVPFAVKTLGTAAGVMITASHNPAAYNGYKVYWGNGCAIIPPHDKGIAACI 180
               +  TPLV F V  LG AAG+++TASHNP  YNGYKVYWGNG  IIPPHD GIAA I
Sbjct: 121 LTSKVAPTPLVAFGVLHLGAAAGIVVTASHNPPQYNGYKVYWGNGAQIIPPHDTGIAARI 180

Query: 181 E------KNLTPITWDKNLVENHKLADRDFAVGLLKNYWSQLHEFHSENNFSLEMKS--- 231
           E       ++ P+   +  VE  KL        +L+  + Q +     N   L+  +   
Sbjct: 181 ELAANSPVDMLPL---ETAVETGKLV-------MLEEDYYQAYRQGVLNAEVLQSPARPE 230

Query: 232 -LKFVYTPIHGVGLPFVTSALHLFGEQGDMISVPLQDSPNPDFPTVKFPNPEEEGALDLA 290
            +   YT +HGVG     + L   G    + SV  Q  P+ DFPTV FPNPEE GA+ L 
Sbjct: 231 LVSLAYTAMHGVGAEMAETLLKDIGVT-QVYSVAAQREPDGDFPTVNFPNPEEAGAMVLV 289

Query: 291 YEQADANGISYVLATDPDADRFAFAEK---------INGAWRRFTGDEVGCILAYFIFQE 341
             +A  +G     A DPDADRFA A +          + A++  TGD+VG +L +++   
Sbjct: 290 MAEAHKHGAMLACANDPDADRFAVAVRKPAATPEMLASEAYQMLTGDQVGVLLGHYLLSH 349

Query: 342 YKNVGKPIDDFYVLSTTVSSAMVKSMAKVEGFHHVETLTGFKWLGNKALELEKQGKFIGL 401
             +     D   +  T VSS+++  +++  G     TLTGFKWL N  +  + Q      
Sbjct: 350 ASD-----DQRLLCCTIVSSSLLTRISEACGARCETTLTGFKWLTNVGMSKQTQENRFLF 404

Query: 402 AYEEALGYMVGSIVRDKDGVNALITFLHLLKRLQLQNLSITEVFEQMSKKYGYYTTQNSY 461
           AYEEALGY VGS+V DKDG++AL+ F+ L   L  +  ++ +  E + ++YGYY  +   
Sbjct: 405 AYEEALGYTVGSMVWDKDGLSALVAFVQLTAELAAKGETLWDRLETIYRQYGYYLNRQVS 464

Query: 462 FLSRDTPKLRALVDALRHYDTKSGYPATLGSKKITNVRDLTTGYDSSSTDGKATLPVSKS 521
                 P    + + LR  D     P+ +  + + +V D++ G    +   + T+ + + 
Sbjct: 465 IALSGEPGAPTIGEQLRALD-----PSEIAGRALVSVDDISLGVRRFADGREETIDLPR- 518

Query: 522 SDNVTFELENGEVIMTIRTSGTEPKLK-FYICARGHSLEDSIKNATEVKQAIKSEWFHPQ 580
           SD + + L+ G   + +R SGTEPK+K +Y        ++ + +     +A  +E+    
Sbjct: 519 SDVLIYRLQ-GNARVIVRPSGTEPKVKCYYEVVEPFGEQEGLADVQRRAEAAMAEFVSRH 577

Query: 581 QNGL 584
           Q GL
Sbjct: 578 QAGL 581


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: 738
Number of extensions: 28
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: 587
Length of database: 584
Length adjustment: 37
Effective length of query: 550
Effective length of database: 547
Effective search space:   300850
Effective search space used:   300850
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