GapMind for catabolism of small carbon sources

 

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

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 Pf1N1B4_1382 Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1)

Query= TCDB::Q9L3M3
         (381 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1382 Branched-chain amino
           acid ABC transporter, amino acid-binding protein (TC
           3.A.1.4.1)
          Length = 377

 Score =  332 bits (852), Expect = 8e-96
 Identities = 177/362 (48%), Positives = 232/362 (64%), Gaps = 5/362 (1%)

Query: 2   KKSLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGI 61
           KK  L A+A+   L  S  A AD+ I VAGP+TG NAAFG Q  KGA+ AA  +NAAGG+
Sbjct: 7   KKGFL-ALAVATALGVSAFAQADIKIGVAGPMTGANAAFGEQYMKGAQAAADAVNAAGGV 65

Query: 62  NGEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHP 121
           NGE+I +  GDD  +PKQ ++VA       V  V+GHF S  +IPASE+Y E GI+   P
Sbjct: 66  NGEKIVLVKGDDACEPKQAVTVAKDLTNQKVAGVVGHFCSSSTIPASEIYDEAGIIAITP 125

Query: 122 GRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETK 181
           G   P +   GL   FR CGRDDQQG +AG Y+ D  K  K+ V+HDK  YGQGLAD TK
Sbjct: 126 GSTNPAVTERGLSAMFRMCGRDDQQGIVAGDYIVDVLKGKKVVVLHDKDTYGQGLADATK 185

Query: 182 KAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLK 241
             +   GVT V+YEG+  G+KDFS ++ K++ AG  ++Y+GGLH EAG ++RQ  +QGLK
Sbjct: 186 AQLAKRGVTPVLYEGLTRGEKDFSTIVTKIRGAGADVVYFGGLHPEAGPLVRQLREQGLK 245

Query: 242 -ATLVSGDGIVSNELASIAG--DAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEAYT 298
               +S DGIV++EL + AG    V G L TFG DP   P +K +V+ F+  G  PE YT
Sbjct: 246 DVKFMSDDGIVTDELVTTAGGPQFVDGVLMTFGADPRLLPDSKTVVDDFRKKGTEPEGYT 305

Query: 299 LYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEW 358
           LY+YA++QT+A A   A S   E  A  +K K P  TV+G+ ++D KGD KI  Y++Y+W
Sbjct: 306 LYAYASVQTLAAAFNGAKSNKGEEAAAWLK-KNPVKTVMGEKTWDSKGDLKISDYVVYQW 364

Query: 359 KK 360
            K
Sbjct: 365 DK 366


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: 452
Number of extensions: 20
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: 381
Length of database: 377
Length adjustment: 30
Effective length of query: 351
Effective length of database: 347
Effective search space:   121797
Effective search space used:   121797
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 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