GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AZOBR_RS08260 in Magnetospirillum magneticum AMB-1

Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate WP_011385357.1 AMB_RS15010 branched-chain amino acid ABC transporter substrate-binding protein

Query= uniprot:G8ALJ3
         (366 letters)



>lcl|NCBI__GCF_000009985.1:WP_011385357.1 AMB_RS15010 branched-chain
           amino acid ABC transporter substrate-binding protein
          Length = 366

 Score =  460 bits (1184), Expect = e-134
 Identities = 222/354 (62%), Positives = 270/354 (76%)

Query: 9   VAVAATAMTASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQKLKL 68
           + +AA  + A  A+ADI +  AGP++G  A FGEQ K+G  +AV DINA GGVLGQKL L
Sbjct: 9   ITLAAALLMAGAARADITIGVAGPLSGSEAAFGEQFKRGAMKAVEDINAKGGVLGQKLAL 68

Query: 69  EVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPASTNPKL 128
            +GDDACDPKQAVAVAN++A   V FVAGHFCSGSSIPAS+VYAE G+LQISPASTNPK 
Sbjct: 69  TLGDDACDPKQAVAVANEMAAKKVPFVAGHFCSGSSIPASEVYAETGILQISPASTNPKF 128

Query: 129 TEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKALNAGG 188
           TE+ L N+FR CGRDDQQG IA  Y+ ++ K K VAI+HDKSAYGKGLAD+T+ AL   G
Sbjct: 129 TERGLPNIFRTCGRDDQQGVIAADYIAKHQKDKVVAIVHDKSAYGKGLADQTRDALGKAG 188

Query: 189 QKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAPIVSGD 248
            K  +YEA +AGEKDYSALV+KLK   VD++Y GGY TEAGL+ RQ++DQG+   ++ GD
Sbjct: 189 IKAALYEAISAGEKDYSALVTKLKASKVDLLYFGGYKTEAGLIVRQLRDQGMQTRLMGGD 248

Query: 249 ALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEKFRKAGYEPEGYTLYTYAALQIW 308
           ALVT EYWAITG AGE TMMTF PDPR+ P   + V+ +R   YEPE YTLYTY  +Q W
Sbjct: 249 ALVTEEYWAITGAAGEGTMMTFSPDPRKNPANADLVKYYRAQKYEPEAYTLYTYGTIQAW 308

Query: 309 AEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWNNGQY 362
           A+AA++A +TD  K+A VL+   ++T IGKIGFDAKGDV +P YV Y W  G+Y
Sbjct: 309 AQAAEKAKTTDWKKVAAVLKAEKFDTAIGKIGFDAKGDVAAPGYVMYVWKGGKY 362


Lambda     K      H
   0.312    0.129    0.366 

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: 438
Number of extensions: 13
Number of successful extensions: 1
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: 366
Length of database: 366
Length adjustment: 30
Effective length of query: 336
Effective length of database: 336
Effective search space:   112896
Effective search space used:   112896
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 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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