GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5505 in Burkholderia phytofirmans PsJN

Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate BPHYT_RS22525 BPHYT_RS22525 dioxygenase

Query= TCDB::Q9HT68
         (260 letters)



>FitnessBrowser__BFirm:BPHYT_RS22525
          Length = 279

 Score =  160 bits (406), Expect = 2e-44
 Identities = 96/253 (37%), Positives = 140/253 (55%), Gaps = 4/253 (1%)

Query: 4   LLAAFSAVAALGLTAAQAAES--LTVAATPVPHAEILNVVKPLLAKEGVDLKIKEFTDYV 61
           L++AF     L  T A AA+S  L +     P  E L +      ++G+D+KI EFTD+ 
Sbjct: 19  LISAFGLALVLQATPASAADSPTLKIGTATSPQIEALKIAAREAKEQGLDVKIIEFTDWN 78

Query: 62  QPNVQVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKLDELPSG 121
            PN  ++ K +D N+FQH P+L+   K  G + VA+    I  +G YS K K+ DEL  G
Sbjct: 79  TPNAALANKDIDVNYFQHIPFLENAKKQGGYNFVAIAPGTIMKIGLYSKKIKRFDELKDG 138

Query: 122 ATVVIPNDATNGGRALLLLDKAGVIKLKDNKSITATPKDIVDNPKNIKIRELEAATLPRV 181
           ATV I ND  NGGR LLLL +AG+IKLK      AT  DI+DNPK++KI +LEA+ L R 
Sbjct: 139 ATVAIANDPVNGGRGLLLLQRAGLIKLKPGIDYRATTLDIIDNPKHLKIVQLEASQLARS 198

Query: 182 LTQVDMALINTNYALEAKLNPTKDALAIEGSDSP-YVNILVARPDNKDSDAMQK-LAKAL 239
           L  VD+A    ++   A       AL  +G ++  Y    V RP++ +   ++K +A   
Sbjct: 199 LDDVDLAQGYPSFIKLAGTTDPNSALLFDGLENKNYAIQWVVRPESANDPRIRKFIAIYQ 258

Query: 240 HSAEIKQFIQEKY 252
           HS  ++  + + +
Sbjct: 259 HSPAVRAALDKAF 271


Lambda     K      H
   0.314    0.131    0.354 

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: 177
Number of extensions: 9
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: 260
Length of database: 279
Length adjustment: 25
Effective length of query: 235
Effective length of database: 254
Effective search space:    59690
Effective search space used:    59690
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 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