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

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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources