GapMind for catabolism of small carbon sources

 

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

Align Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale)
to candidate WP_011385357.1 AMB_RS15010 branched-chain amino acid ABC transporter substrate-binding protein

Query= uniprot:A0A160A0J6
         (375 letters)



>NCBI__GCF_000009985.1:WP_011385357.1
          Length = 366

 Score =  285 bits (730), Expect = 1e-81
 Identities = 148/357 (41%), Positives = 220/357 (61%), Gaps = 6/357 (1%)

Query: 11  LFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGSKMAIEQINAKGGVNGKQ 70
           L AA+++AG A     AD I IG+AGP +G  A +G+    G+  A+E INAKGGV G++
Sbjct: 11  LAAALLMAGAAR----AD-ITIGVAGPLSGSEAAFGEQFKRGAMKAVEDINAKGGVLGQK 65

Query: 71  LVAVEYDDACDPKQAVAVANKVVNDGIKFVVGHLCSSSTQPASDIYEDEGVVMITPAATS 130
           L     DDACDPKQAVAVAN++    + FV GH CS S+ PAS++Y + G++ I+PA+T+
Sbjct: 66  LALTLGDDACDPKQAVAVANEMAAKKVPFVAGHFCSGSSIPASEVYAETGILQISPASTN 125

Query: 131 PDITARGYKMIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIASAVKKTLE 190
           P  T RG   IFRT G D  QG  A +YIA H K K+VA++HDK  YG+G+A   +  L 
Sbjct: 126 PKFTERGLPNIFRTCGRDDQQGVIAADYIAKHQKDKVVAIVHDKSAYGKGLADQTRDALG 185

Query: 191 DKGVKVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQSQEKGLKAKFM 250
             G+K A++E ++AG+KD+S+++ KLK + VD +Y+GGY  E GLI+RQ +++G++ + M
Sbjct: 186 KAGIKAALYEAISAGEKDYSALVTKLKASKVDLLYFGGYKTEAGLIVRQLRDQGMQTRLM 245

Query: 251 GPEGVGNDSISQIAKESSEGLLVTLPKSFDQDPANIALADAFKAKKEDPSGPFVFPSYSA 310
           G + +  +    I   + EG ++T      ++PAN  L   ++A+K +P   +   +Y  
Sbjct: 246 GGDALVTEEYWAITGAAGEGTMMTFSPDPRKNPANADLVKYYRAQKYEPEA-YTLYTYGT 304

Query: 311 VTVIADAIKAAKSEDAGKVAEAIHAGTFKTPTGDLSFDKNGDLKDFKFVVYEWHFGK 367
           +   A A + AK+ D  KVA  + A  F T  G + FD  GD+    +V+Y W  GK
Sbjct: 305 IQAWAQAAEKAKTTDWKKVAAVLKAEKFDTAIGKIGFDAKGDVAAPGYVMYVWKGGK 361


Lambda     K      H
   0.314    0.132    0.372 

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: 367
Number of extensions: 17
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: 375
Length of database: 366
Length adjustment: 30
Effective length of query: 345
Effective length of database: 336
Effective search space:   115920
Effective search space used:   115920
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: 49 (23.5 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