GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmB in Herbaspirillum seropedicae SmR1

Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate HSERO_RS00780 HSERO_RS00780 sugar transferase

Query= SwissProt::O06995
         (226 letters)



>FitnessBrowser__HerbieS:HSERO_RS00780
          Length = 215

 Score = 56.6 bits (135), Expect = 4e-13
 Identities = 53/192 (27%), Positives = 79/192 (41%), Gaps = 21/192 (10%)

Query: 4   VIFDLDGVITDTAEYHFLAWKHIAEQIDIPFD-RDMNERLKGISREESLESILIFGGAET 62
           VIFD DG + D+      AW        +     D   R +G+S    +  +    G   
Sbjct: 11  VIFDCDGTLVDSEVVAARAWSEYVATYGVQLTPEDALARFRGVSMSWCIAHVAQLRG--- 67

Query: 63  KYTNAEKQELMHRKNRDYQMLISKLTPEDLLPGIGRLLCQLKNENIKIGLASSSRNAPK- 121
                  Q L     ++ +  +  +  + L P I   L  ++   I   LAS   NAP  
Sbjct: 68  -------QALPAHFEQELRARMGVMLEQHLQP-INGALEMVEQLQIPFALAS---NAPHH 116

Query: 122 ----ILRRLAIIDDFHA-IVDPTTLAKGKPDPDIFLTAAAMLDVSPADCAAIEDAEAGIS 176
                LR   ++  FH  I     + + KPDP +FL AA  L V PA CA +ED+  G+ 
Sbjct: 117 KIELCLRVTGLLPHFHGRIFSAYDVQRWKPDPALFLFAAERLGVPPARCAVVEDSLPGVQ 176

Query: 177 AIKSAGMFAVGV 188
           A  +AGM  + +
Sbjct: 177 AGLAAGMKVIAL 188


Lambda     K      H
   0.319    0.136    0.390 

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: 124
Number of extensions: 6
Number of successful extensions: 2
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: 226
Length of database: 215
Length adjustment: 22
Effective length of query: 204
Effective length of database: 193
Effective search space:    39372
Effective search space used:    39372
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 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