GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM in Paraburkholderia bryophila 376MFSha3.1

Align Histidine transport system permease protein HisM (characterized)
to candidate H281DRAFT_00222 H281DRAFT_00222 amino acid ABC transporter membrane protein 2, PAAT family

Query= SwissProt::P0A2I7
         (235 letters)



>FitnessBrowser__Burk376:H281DRAFT_00222
          Length = 237

 Score =  343 bits (881), Expect = 1e-99
 Identities = 166/232 (71%), Positives = 201/232 (86%)

Query: 1   MIEIIQEYWKSLLWTDGYRFTGVAITLWLLISSVVMGGLLAVILAVGRVSSNKFIRFPIW 60
           MIEIIQEYW++ L+TDGYRFTG+AITLWLL+ S+ +G  L++ LAV RVS  K++   +W
Sbjct: 1   MIEIIQEYWRNYLYTDGYRFTGLAITLWLLVVSIGLGFCLSIPLAVARVSKKKWLSTLVW 60

Query: 61  LFTYIFRGTPLYVQLLVFYSGMYTLEIVKGTDLLNAFFRSGLNCTVLALTLNTCAYTTEI 120
           L+TYIFRGTPLYVQLL+ Y+G+Y+LEIV+  +L NAFFR G+NCT+LA TLNTCAYTTEI
Sbjct: 61  LYTYIFRGTPLYVQLLLCYTGLYSLEIVRNHELTNAFFREGMNCTLLAFTLNTCAYTTEI 120

Query: 121 FAGAIRSVPHGEIEAARAYGFSSFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTA 180
           FAGAI++ P+GEIEAARAYG SSF +YR +ILPSALR ALP YSNEVILMLH+T +AFTA
Sbjct: 121 FAGAIKATPYGEIEAARAYGMSSFTLYRRVILPSALRRALPYYSNEVILMLHATTVAFTA 180

Query: 181 TVPDLLKIARDINSATYQPFTAFGIAAVLYLLISYVLISLFRRAERRWLQHV 232
           TVPD+LKIARD+NSATYQ F AFGIAA+LYL IS+ L+ LFRRAERRWL ++
Sbjct: 181 TVPDILKIARDVNSATYQSFNAFGIAALLYLCISFALVWLFRRAERRWLAYL 232


Lambda     K      H
   0.330    0.141    0.429 

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: 274
Number of extensions: 7
Number of successful extensions: 1
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: 235
Length of database: 237
Length adjustment: 23
Effective length of query: 212
Effective length of database: 214
Effective search space:    45368
Effective search space used:    45368
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 46 (22.3 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