GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011385357.1
          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 (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