GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braE in Pseudomonas fluorescens FW300-N2E2

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Pf6N2E2_2924 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Query= uniprot:Q1MCU1
         (463 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2924 Branched-chain amino
           acid transport system permease protein LivM (TC
           3.A.1.4.1)
          Length = 418

 Score =  354 bits (908), Expect = e-102
 Identities = 217/440 (49%), Positives = 278/440 (63%), Gaps = 36/440 (8%)

Query: 20  LTEALFAAVLSFGMFVLYVGLKTDQNISNELIIVQRWGLLAIFVAVAAIGRFAMVVFIRP 79
           L  ALF+A+L + +    +GLK      N  +      +LA  +AV ++  F  V+F   
Sbjct: 5   LKSALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAILAT-IAVCSLLMFLRVLF--- 60

Query: 80  NIDRRKLSKAREGELDISTEKSFF------HRHFLKIALIALLLYPMVVVAIKGPQGSLT 133
           +     + K+  G   I  + S F       R  +   ++  L++P       G +G++ 
Sbjct: 61  STQISAMWKSSPGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFF-----GSRGAV- 114

Query: 134 YVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLP 193
              +    ILIYVML  GLNIVVGLAGLLDLGYV FYAVGAYSYALLS YFGLSFW+ LP
Sbjct: 115 ---DIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLP 171

Query: 194 LSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKAT 253
           ++G+ AA +G +LGFPVLRLRGDYLAIVTL FGEIIRL L N TD+T G  GIS+I K T
Sbjct: 172 IAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPT 231

Query: 254 LFGIPFDATAGGFAKLFH----LPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRA 309
            FG+ F+  A    + FH    L  +S    IFL+ + L L +   +V  RL RMPIGRA
Sbjct: 232 FFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRA 291

Query: 310 WEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVI 369
           WEALREDEIACR+LG+N    KL+AF  GA FAGFAGSFFAARQG V+PESF F+ESA+I
Sbjct: 292 WEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAII 351

Query: 370 LAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVV 429
           LAIVVLGGMGS  G+ +AAIVM+   E++RE S              YRML+FG  MV++
Sbjct: 352 LAIVVLGGMGSQLGVILAAIVMILLPEMMREFS-------------EYRMLMFGALMVLM 398

Query: 430 MLFKPRGFVGSREPTAFLRE 449
           M+++P+G +  + P   LR+
Sbjct: 399 MIWRPQGLLPMQRPHMELRK 418


Lambda     K      H
   0.330    0.145    0.432 

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: 638
Number of extensions: 40
Number of successful extensions: 3
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: 463
Length of database: 418
Length adjustment: 32
Effective length of query: 431
Effective length of database: 386
Effective search space:   166366
Effective search space used:   166366
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 (21.8 bits)
S2: 51 (24.3 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, the preprint 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