GapMind for Amino acid biosynthesis

 

Alignments for a candidate for split_metH_3 in Marivita geojedonensis DPG-138

Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate WP_085639258.1 MGEO_RS14540 methyltetrahydrofolate cobalamin methyltransferase

Query= reanno::Phaeo:GFF1582
         (353 letters)



>NCBI__GCF_002115805.1:WP_085639258.1
          Length = 360

 Score =  563 bits (1450), Expect = e-165
 Identities = 290/360 (80%), Positives = 310/360 (86%), Gaps = 7/360 (1%)

Query: 1   MTRTVVESKTKTAILGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGA 60
           MTRT+VESKTKTAI+GFD+PFCVIGERINPTGRK L  ELE GDFS VE DALAQV AGA
Sbjct: 1   MTRTIVESKTKTAIIGFDQPFCVIGERINPTGRKILNEELERGDFSRVEADALAQVAAGA 60

Query: 61  NILDINAGVVYNSN-------PNPNETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAG 113
           NILDIN+G V+++         + N  EP LM ++VE VQ +TD PLCIDSSVPGALE G
Sbjct: 61  NILDINSGAVFSNKMAEDPRYADNNFVEPTLMKELVERVQAVTDCPLCIDSSVPGALENG 120

Query: 114 LQAAEGRPLLNSVTGEEERLEHVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVE 173
           L AAEGRPLLNSVTGEEERLE VLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVE
Sbjct: 121 LAAAEGRPLLNSVTGEEERLELVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVE 180

Query: 174 RAADFGIPAHDIVVDPLVMPIGAMATAGQQVFALVRRLREELGVNTTCGASNVSFGLPNR 233
           RAADFGIPAHDIVVDPLVMPIGAM TAG QVF LVRRLREELGVNTTCGASN+SFGLPNR
Sbjct: 181 RAADFGIPAHDIVVDPLVMPIGAMGTAGLQVFTLVRRLREELGVNTTCGASNISFGLPNR 240

Query: 234 HGINNAFLPMAMGAGMTSAIMNPVALPITQKKIAEKKAEVEAAGIILPEGMEDEAFVQMF 293
           HGINNAFLPMAMGAGMTSAIMNPVALP+   KIAEK+AEV AAGI+LPE M+DE F  +F
Sbjct: 241 HGINNAFLPMAMGAGMTSAIMNPVALPVGPTKIAEKRAEVAAAGIMLPEDMDDETFCTIF 300

Query: 294 GLGSTKPRAGKEMEAIRAANLLTNNDPHGGEWIKANKEPAKEGEEGRGRGGRAGGRRRRA 353
           GLGSTKPR GKEMEAIRAAN LTNND  GG WI  N++P K G+EGRGR GR GGRRRRA
Sbjct: 301 GLGSTKPRPGKEMEAIRAANFLTNNDEGGGAWIAFNRQPPKAGQEGRGREGRTGGRRRRA 360


Lambda     K      H
   0.315    0.134    0.379 

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: 453
Number of extensions: 16
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: 353
Length of database: 360
Length adjustment: 29
Effective length of query: 324
Effective length of database: 331
Effective search space:   107244
Effective search space used:   107244
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 Jul 26 2024. The underlying query database was built on Jul 25 2024.

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