GapMind for catabolism of small carbon sources

 

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

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_043744689.1 AMB_RS14985 transcriptional regulator

Query= reanno::SB2B:6938110
         (299 letters)



>lcl|NCBI__GCF_000009985.1:WP_043744689.1 AMB_RS14985
           transcriptional regulator
          Length = 297

 Score =  291 bits (746), Expect = 9e-84
 Identities = 155/296 (52%), Positives = 186/296 (62%), Gaps = 8/296 (2%)

Query: 2   MRMGVDLGGTKIELVALGEDGSELFRKRIATPR-EYQGTLNAVVTLVNEAEATLGTQGSL 60
           +R+G+DLGGTK E +AL   G EL R+R+AT R  Y GT+  +  LV   E+ LG   S+
Sbjct: 3   LRIGIDLGGTKTEAIALDLSGRELARQRVATARGSYDGTIATIKGLVEGLESRLGAAASV 62

Query: 61  GIGIPGVISPYTGLVKNANSTWINGHPLDRDLGALLNREVRVANDANCFAVSEAVDGAAA 120
           GIGIPG ISP TGL+KNANSTW+ G PLDRDL   L R VR+ANDA+CFA+SEA DGA A
Sbjct: 63  GIGIPGTISPRTGLIKNANSTWLIGKPLDRDLETALGRPVRLANDADCFALSEATDGAGA 122

Query: 121 GKRVVFGAILGTGCGAGLAFDGRVHEGGNGIGGEWGHNPLPWMRPDEFNTTECFCGNKDC 180
           G   VFG ILGTG G G+   GR+  G N I GEWGHNPLPW    E     C+CG   C
Sbjct: 123 GFDTVFGVILGTGVGGGIVAHGRLLSGPNAIAGEWGHNPLPWPEDAERPGPACYCGRSGC 182

Query: 181 IETFVSGTGFVRDFRNSGGTAQNGAEIMSLVDAGDELANLVFDRYLDRLARSLAHVINML 240
           IETF+SG G  RD    GG    G     L  + D  A     RY  RLAR+LA VIN++
Sbjct: 183 IETFLSGPGLARD---HGG----GLSAEQLATSDDAAAGAALARYERRLARALAAVINVI 235

Query: 241 DPDAIVLGGGMSNVQAIYARLPAILPKYVVGRECRTPVVQNLYGCSSGVRGAAWLW 296
           DP  IVLGGG+S +  +Y  +PA+   +V      T +    +G SSGVRGAAWLW
Sbjct: 236 DPHVIVLGGGLSKLDRLYRNVPALWEGFVFSDHVDTLLRPPRHGDSSGVRGAAWLW 291


Lambda     K      H
   0.320    0.139    0.429 

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: 306
Number of extensions: 16
Number of successful extensions: 3
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: 299
Length of database: 297
Length adjustment: 27
Effective length of query: 272
Effective length of database: 270
Effective search space:    73440
Effective search space used:    73440
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 (21.8 bits)
S2: 48 (23.1 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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