GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Magnetospirillum magneticum AMB-1

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 WP_011385357.1 AMB_RS15010 branched-chain amino acid ABC transporter substrate-binding protein

Query= TCDB::Q9L3M3
         (381 letters)



>NCBI__GCF_000009985.1:WP_011385357.1
          Length = 366

 Score =  368 bits (945), Expect = e-106
 Identities = 183/359 (50%), Positives = 244/359 (67%), Gaps = 1/359 (0%)

Query: 1   MKKSLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGG 60
           M ++ ++ + L A L  +G A AD+ I VAGPL+G  AAFG Q ++GA +A  DINA GG
Sbjct: 1   MSRTGITGITLAAALLMAGAARADITIGVAGPLSGSEAAFGEQFKRGAMKAVEDINAKGG 60

Query: 61  INGEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNH 120
           + G+++ + LGDD  DPKQ ++VAN+ AA  V FV GHF SG SIPASEVYAE GIL+  
Sbjct: 61  VLGQKLALTLGDDACDPKQAVAVANEMAAKKVPFVAGHFCSGSSIPASEVYAETGILQIS 120

Query: 121 PGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADET 180
           P    P     GL N FRTCGRDDQQG IA  Y+A H KD  +A+VHDK+ YG+GLAD+T
Sbjct: 121 PASTNPKFTERGLPNIFRTCGRDDQQGVIAADYIAKHQKDKVVAIVHDKSAYGKGLADQT 180

Query: 181 KKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGL 240
           + A+  AG+   +YE I+ G+KD+SAL+ K+K + V ++Y+GG  TEAGLI+RQ  DQG+
Sbjct: 181 RDALGKAGIKAALYEAISAGEKDYSALVTKLKASKVDLLYFGGYKTEAGLIVRQLRDQGM 240

Query: 241 KATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEAYTLY 300
           +  L+ GD +V+ E  +I G A  GT+ TF PDP  NPAN +LV+ ++A  + PEAYTLY
Sbjct: 241 QTRLMGGDALVTEEYWAITGAAGEGTMMTFSPDPRKNPANADLVKYYRAQKYEPEAYTLY 300

Query: 301 SYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWK 359
           +Y  +Q  A AA+ A + D + VA  +K +  F T +G I FD KGD   PGY+MY WK
Sbjct: 301 TYGTIQAWAQAAEKAKTTDWKKVAAVLKAE-KFDTAIGKIGFDAKGDVAAPGYVMYVWK 358


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: 412
Number of extensions: 23
Number of successful extensions: 2
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: 366
Length adjustment: 30
Effective length of query: 351
Effective length of database: 336
Effective search space:   117936
Effective search space used:   117936
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 (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