GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00895 in Magnetospirillum magneticum AMB-1

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_083763604.1 AMB_RS09125 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC86
         (260 letters)



>lcl|NCBI__GCF_000009985.1:WP_083763604.1 AMB_RS09125 ABC
           transporter ATP-binding protein
          Length = 257

 Score =  208 bits (530), Expect = 8e-59
 Identities = 117/249 (46%), Positives = 156/249 (62%), Gaps = 11/249 (4%)

Query: 18  RFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELAGKPYEPTA 77
           RFGGL A++D+  +    ++  +IGPNGAGKTT FN ITG Y P  G   L   P  P  
Sbjct: 2   RFGGLFAVNDLSFSAAPKEITAVIGPNGAGKTTLFNCITGFYKPQVGRMTL-DHPSGPML 60

Query: 78  VHEV------AKAGIARTFQNIRLFAEMTALENVMVGRH---IRTGSGLFGAVFRTKGFK 128
           +  +      AKAG+ARTFQNIRLFA M+ LEN++V +H   +R  +     +     + 
Sbjct: 61  LERLDDFAISAKAGVARTFQNIRLFARMSVLENLIVAQHTTLMRASAFSLAGLLGLSRYA 120

Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188
             EA   +RA+  LD VG+   AD +A +L YG QRRLEIARA+ T P L+ LDEPAAG+
Sbjct: 121 RAEARAVERARHWLDKVGLTSLADEEAGSLPYGHQRRLEIARAMCTGPLLLCLDEPAAGL 180

Query: 189 NATEKVQLRELIDRIRNDNRT-ILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKN 247
           N  E  +L  L+  IR++N   +LLIEHD+ +VM + D + VLDYGK+IAEG PA ++ +
Sbjct: 181 NPRESAELNRLLLDIRDENGIGLLLIEHDMSVVMEISDHIVVLDYGKKIAEGAPAAIKAD 240

Query: 248 EKVIEAYLG 256
             VI AYLG
Sbjct: 241 PAVIRAYLG 249


Lambda     K      H
   0.319    0.137    0.384 

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: 211
Number of extensions: 11
Number of successful extensions: 4
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: 260
Length of database: 257
Length adjustment: 24
Effective length of query: 236
Effective length of database: 233
Effective search space:    54988
Effective search space used:    54988
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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