GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livM in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_4609 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Query= TCDB::P21628
         (417 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4609
           Branched-chain amino acid transport system permease
           protein LivM (TC 3.A.1.4.1)
          Length = 418

 Score =  606 bits (1563), Expect = e-178
 Identities = 308/417 (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   MTRNLKQALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSDATLITIAVCSVLMFLRVLF 60

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

Query: 121 LIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALF 180
           LIYVMLG+GLNIVVGLAGLLDLGYVGFYAVGAY+YALL+ Y G  FW  LPIAG+MAA F
Sbjct: 121 LIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYYGLSFWICLPIAGLMAATF 180

Query: 181 GFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERR 240
           GFLLGFPVLRLRGDYLAIVTLGFGEIIR+ LRN+T +TGGPNGI +I KPT FGLTFER+
Sbjct: 181 GFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTGLTGGPNGISNIEKPTFFGLTFERK 240

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

Query: 301 ACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGM 360
           ACRALGLNPT++KLSAFT+GASFAGFAGSFFAARQGLVTPESFTFIESA+ILAIVVLGGM
Sbjct: 301 ACRALGLNPTVIKLSAFTLGASFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGM 360

Query: 361 GSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLELK 416
           GSQLGVILAAVVM+LL E MR F+EYRML+FG  M++MMIWRPQGLLPMQRPH+EL+
Sbjct: 361 GSQLGVILAAVVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMELR 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: 659
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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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