GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Pseudomonas fluorescens FW300-N2C3

Align BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC (characterized)
to candidate AO356_08500 AO356_08500 amino acid ABC transporter substrate-binding protein

Query= TCDB::Q9L3M3
         (381 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_08500
          Length = 378

 Score =  330 bits (847), Expect = 3e-95
 Identities = 180/363 (49%), Positives = 232/363 (63%), Gaps = 6/363 (1%)

Query: 2   KKSLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGI 61
           KK  L A+A+ A L  S  A ADV   VAGP+TG NAAFG Q  KGA+ AA  IN AGG+
Sbjct: 7   KKGFL-ALAVAAALGVSAFAQADVKFGVAGPMTGANAAFGEQYMKGAQAAADAINKAGGV 65

Query: 62  NGEQIKIELGDDVSDPKQGISVANKFA-ADGVKFVIGHFNSGVSIPASEVYAENGILRNH 120
           NGE+I +  GDD  +PKQ ++VAN+    D V  V+GHF S  +IPASEVY E GI+   
Sbjct: 66  NGEKIVLVAGDDACEPKQAVAVANRLVDQDKVIGVVGHFCSSNTIPASEVYDEAGIIAIT 125

Query: 121 PGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADET 180
           PG   P +   GL   FR CGRDDQQG +AG Y+ D  K  K+AV+HDK  YGQGLAD T
Sbjct: 126 PGSTNPQVTERGLSAMFRMCGRDDQQGIVAGDYIVDVLKGKKVAVLHDKDTYGQGLADAT 185

Query: 181 KKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGL 240
           K  +   GV EV+YEG+  G+KDFSA++ K++  G  ++Y+GGLH EAG ++RQ  +QGL
Sbjct: 186 KAQLAKRGVKEVLYEGLTRGEKDFSAVVTKIRSVGADVVYFGGLHPEAGPLVRQLREQGL 245

Query: 241 K-ATLVSGDGIVSNELASIAGDA--VAGTLNTFGPDPTANPANKELVEKFKAAGFNPEAY 297
           K    +S DGIV++EL + AG A  V G   TFG DP   P +K +VE+F+  G  PE Y
Sbjct: 246 KDVKFMSDDGIVTDELVTTAGGAQYVDGVYMTFGADPRLLPDSKAVVEEFRKNGTEPEGY 305

Query: 298 TLYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYE 357
           TLY+YA++Q +A     A S   E  AK +K   P  TV+G   +D KGD K+  Y++Y+
Sbjct: 306 TLYAYASVQALAAGFNGAKSNKGEDAAKWLK-ANPVQTVMGKKEWDTKGDLKVSDYVVYQ 364

Query: 358 WKK 360
           W K
Sbjct: 365 WDK 367


Lambda     K      H
   0.314    0.132    0.383 

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: 469
Number of extensions: 22
Number of successful extensions: 4
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: 381
Length of database: 378
Length adjustment: 30
Effective length of query: 351
Effective length of database: 348
Effective search space:   122148
Effective search space used:   122148
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 (22.0 bits)
S2: 50 (23.9 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