GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braE in Pseudomonas fluorescens FW300-N1B4

Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate Pf1N1B4_3216 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Query= TCDB::P21628
         (417 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3216 Branched-chain amino
           acid transport system permease protein LivM (TC
           3.A.1.4.1)
          Length = 418

 Score =  607 bits (1566), Expect = e-178
 Identities = 305/417 (73%), Positives = 354/417 (84%), Gaps = 1/417 (0%)

Query: 1   MSQSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWTIAAAALAMFVWQLF 60
           M+++LK+ALFSALLV  V+YP+LGLKL  VGI LEV G    TL TIA  ++ MF+  LF
Sbjct: 1   MTRNLKQALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSTATLITIAVCSVLMFLRVLF 60

Query: 61  RDRIPLKLGRGVGYKVNGSGLKNFLSLPSTQRWAVLALVVVAFVWPFFASRGAVDIATLI 120
             +I           V  +   NFL+LP+TQRW ++AL++ A VWPFF SRGAVDIATL+
Sbjct: 61  DQQISSAWKASPNLPVMPAKATNFLTLPTTQRWIIIALIIGALVWPFFGSRGAVDIATLV 120

Query: 121 LIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALF 180
           LIYVMLG+GLNIVVGLAGLLDLGYVGFYAVGAY+YALL+ Y G  FW  LPIAGMMAA F
Sbjct: 121 LIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYYGLSFWICLPIAGMMAATF 180

Query: 181 GFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERR 240
           GFLLGFPVLRLRGDYLAIVTLGFGEIIR+ LRN+T++TGGPNGI +IPKPTLFGL+F+R 
Sbjct: 181 GFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDLTGGPNGISNIPKPTLFGLSFDRT 240

Query: 241 APEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEV 300
           A EG+QTFHE+FG+ YN+  KVI LY++A+LL L ALFVINRL+RMP+GRAWEALREDE+
Sbjct: 241 AAEGLQTFHEYFGLEYNSINKVIFLYLIAVLLSLFALFVINRLLRMPLGRAWEALREDEI 300

Query: 301 ACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGM 360
           ACRALGLNPT++KLSAFT+GA FAGFAGSFFAARQGLVTPESFTFIESA ILAIVVLGGM
Sbjct: 301 ACRALGLNPTVIKLSAFTLGACFAGFAGSFFAARQGLVTPESFTFIESATILAIVVLGGM 360

Query: 361 GSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLELK 416
           GSQLGV+LAA VM+LL E MR F+EYRML+FG  M++MMIWRPQGLLPMQRPH+EL+
Sbjct: 361 GSQLGVVLAATVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMELR 417


Lambda     K      H
   0.330    0.146    0.439 

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: 652
Number of extensions: 31
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: 417
Length of database: 418
Length adjustment: 32
Effective length of query: 385
Effective length of database: 386
Effective search space:   148610
Effective search space used:   148610
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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 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