GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natE in Burkholderia phytofirmans PsJN

Align NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate BPHYT_RS15590 BPHYT_RS15590 amino acid ABC transporter ATPase

Query= TCDB::Q8YT15
         (247 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS15590 BPHYT_RS15590 amino acid
           ABC transporter ATPase
          Length = 238

 Score =  209 bits (533), Expect = 3e-59
 Identities = 106/236 (44%), Positives = 161/236 (68%), Gaps = 3/236 (1%)

Query: 9   TPLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGK 68
           T +L+++ +   Y   +  ++G++  V  GELVT+IG NGAGK+T  K I GL     G 
Sbjct: 3   TAMLKIKGLQVNY-GGIQAVKGIDLEVAQGELVTLIGANGAGKTTTMKAITGLKPYTIGD 61

Query: 69  ITFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDS--LQPLKDKI 126
           I + G++I G+  + +++ G+  VP+   +F  +S+ EN++MGA++R D+  ++   D++
Sbjct: 62  IEYMGESIKGVPPHLLLKKGLAMVPEGRGIFARMSIVENMQMGAYLRTDTDGIKADVDRM 121

Query: 127 FAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQV 186
           F  FPRL +R  Q AGTLSGGE+QMLAM +A++  P LL+LDEPS  LSPI+V ++FE V
Sbjct: 122 FGFFPRLKERAAQYAGTLSGGEQQMLAMARAIISRPKLLLLDEPSMGLSPIMVEKIFEVV 181

Query: 187 KQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLG 242
           + I+ EG  ++LVEQNAR AL+ A+RGYV++SG   +SG  +++L DPKV   YLG
Sbjct: 182 RAISAEGMTVLLVEQNARLALQAANRGYVMDSGLVTMSGDAKQMLDDPKVRAAYLG 237


Lambda     K      H
   0.317    0.136    0.377 

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: 168
Number of extensions: 7
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: 247
Length of database: 238
Length adjustment: 23
Effective length of query: 224
Effective length of database: 215
Effective search space:    48160
Effective search space used:    48160
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 (21.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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