GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Brevibacterium jeotgali SJ5-8

Align Probable phosphoribomutase; PRM; Phosphoglucomutase 3 homolog; PGM 3 homolog; EC 5.4.2.7 (characterized)
to candidate WP_101589167.1 BJEO58_RS09135 phospho-sugar mutase

Query= SwissProt::O74478
         (587 letters)



>NCBI__GCF_900169175.1:WP_101589167.1
          Length = 617

 Score =  250 bits (639), Expect = 1e-70
 Identities = 204/591 (34%), Positives = 277/591 (46%), Gaps = 84/591 (14%)

Query: 7   ELVDEWFKLDQDETTRNEVSQLIKA----------EDYATLKQIMHPRIGFGTSGLRAEI 56
           ++V  W   D D  TR E+S+L++A          E  A L       + FGT+GLR EI
Sbjct: 14  DVVRAWIADDPDPVTRAELSELLEAATAEAGPASAEALADLTDRFSGPLEFGTAGLRGEI 73

Query: 57  GAGFARMNCLTVIQASQGFAEYLLQTVPSAAK-----LGVVIGHDHRHKSNTFARLTAAV 111
            AG  RMN   VI+A+ G + +L   +  +         VVIG D R+ S  FAR TAAV
Sbjct: 74  AAGPHRMNRAVVIRAAAGLSAFLADHMQDSGPAISQPFTVVIGCDARYGSADFARDTAAV 133

Query: 112 FLQKGFKTYFFDHLVHTPLVPFAVKTLGTAAGVMITASHNPAAYNGYKVYWGN------- 164
               G +       + TP++ FAV+ LG  AGVM+TASHNP   NGYKVY G        
Sbjct: 134 VTAAGGRALLLPAKLPTPVLAFAVQHLGADAGVMVTASHNPPRDNGYKVYLGTRPLIALD 193

Query: 165 ---------GCAIIPPHDKGIAACIEKNLTPITWDKNLVENHKLADRDF-AVG--LLKNY 212
                    G  I+PP D+ IA+ I           + V +   AD  + ++G  +   Y
Sbjct: 194 GPEQAAHGTGAQIVPPADELIASRIAA--------VDAVASVPRADSGWTSLGSEVETAY 245

Query: 213 WSQLHEFHSENNFSLEMKSLKFVYTPIHGVGLPFVTSALHLFGEQGDMISVPLQDSPNPD 272
              L    +E   ++   +L+ V T +HGVG   +  AL   G   D+  V  Q  P+PD
Sbjct: 246 LDSLTRLGAE---AVPRGALRIVTTALHGVGATTLARALGKAGF-ADVRPVESQRDPDPD 301

Query: 273 FPTVKFPNPEEEGALDLAYEQADANGISYVLATDPDADRFAFA--EKINGAWRRFTGDEV 330
           FPTV FPNPEE+GAL+ A   AD      +LA DPDADR + A        W + +GDEV
Sbjct: 302 FPTVAFPNPEEDGALEEATALADHVDAHLILANDPDADRLSAAVPSPDGSGWYQLSGDEV 361

Query: 331 GCILAYFIFQEYKNVGKPIDD--------FYVLSTTVSSAMVKSMAKVEGFHHVETLTGF 382
           G +L   I         P++D            S+ VSS  + ++A   G  H  TLTGF
Sbjct: 362 GLLLGEAIALRLAEAAAPLEDPAAQPALHPVFASSVVSSRALAALAARHGIAHTPTLTGF 421

Query: 383 KWLGNKALELEKQGKFIGLAYEEALGYMVG-SIVRDKDGVNALITFLHLLKRLQLQNLSI 441
           KW+         +   I   YEEALGY V    VRDKDG++A + F     RL+    +I
Sbjct: 422 KWI--------SRVPGIVYGYEEALGYCVDPDTVRDKDGISAALLFAAYTSRLRAAGRTI 473

Query: 442 TEVFEQMSKKYGYYTTQNSYFLSRDTPKLRALVDALRHYDTKSGYPATLGSKKITNVRDL 501
            +   ++    G + TQ   F   DT  +   V  LR     +  P  LG   +T V D+
Sbjct: 474 PDELARIRATDGVFRTQPLTFRLEDTALIAGAVATLR-----ANPPTQLGGSPVTEVIDM 528

Query: 502 TTGY-DSSSTDGKATLPVSKSSDNVTFELENGEVIMTIRTSGTEPKLKFYI 551
           T GY D + TDG   L  +++ D              +R SGTEPKLK Y+
Sbjct: 529 TLGYGDLAPTDGIVVL--TQAGDRA-----------IVRPSGTEPKLKCYL 566


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: 818
Number of extensions: 38
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 587
Length of database: 617
Length adjustment: 37
Effective length of query: 550
Effective length of database: 580
Effective search space:   319000
Effective search space used:   319000
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.

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