GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hisQ in Paraburkholderia bryophila 376MFSha3.1

Align Histidine transport system permease protein HisQ (characterized)
to candidate H281DRAFT_06474 H281DRAFT_06474 amino acid ABC transporter membrane protein 1, PAAT family

Query= SwissProt::P0A2I9
         (228 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_06474 H281DRAFT_06474 amino
           acid ABC transporter membrane protein 1, PAAT family
          Length = 229

 Score =  291 bits (746), Expect = 5e-84
 Identities = 144/228 (63%), Positives = 182/228 (79%)

Query: 1   MLYGFSGVILQGAIVTLELALSSVVLAVLIGLVGAGAKLSQNRVTGLIFEGYTTLIRGVP 60
           +LYGF  V+L G I T+EL++ S+  AV++GL GA AKLS NR    +  GYTTLIR VP
Sbjct: 2   VLYGFGPVLLAGTIQTVELSVLSLAAAVVLGLAGAAAKLSFNRPLRALATGYTTLIRSVP 61

Query: 61  DLVLMLLIFYGLQIALNVVTDSLGIDQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVP 120
           DLVLMLL+FY +QIA+N +TD+L + Q DIDP VAG++TLGFIYGAYFTETFRGAF+AVP
Sbjct: 62  DLVLMLLLFYSIQIAVNNLTDALNLPQFDIDPFVAGVLTLGFIYGAYFTETFRGAFLAVP 121

Query: 121 KGHIEAATAFGFTHGQTFRRIMFPAMMRYALPGIGNNWQVILKATALVSLLGLEDVVKAT 180
           +G +EA +A+G +  + F RI+FP MMR+ALPGIGNNWQV++KATALVS++GL DVVKA 
Sbjct: 122 RGQLEAGSAYGMSGVRVFARILFPQMMRFALPGIGNNWQVLVKATALVSIIGLADVVKAA 181

Query: 181 QLAGKSTWEPFYFAVVCGLIYLVFTTVSNGVLLLLERRYSVGVKRADL 228
           Q AGKST+  F+F ++  LIYL  TTVSN  L+ LERRYS+GV+ A+L
Sbjct: 182 QDAGKSTFNMFFFILIAALIYLALTTVSNLALIWLERRYSIGVRHAEL 229


Lambda     K      H
   0.328    0.144    0.422 

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: 217
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: 228
Length of database: 229
Length adjustment: 23
Effective length of query: 205
Effective length of database: 206
Effective search space:    42230
Effective search space used:    42230
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 (21.7 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, 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