GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4609
          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:

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