GapMind for catabolism of small carbon sources

 

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

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_085638891.1 MGEO_RS13900 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::psRCH2:GFF857
         (371 letters)



>NCBI__GCF_002115805.1:WP_085638891.1
          Length = 362

 Score =  330 bits (845), Expect = 5e-95
 Identities = 185/355 (52%), Positives = 233/355 (65%), Gaps = 4/355 (1%)

Query: 1   MASVTLRDICKSYDGTP-ITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGD 59
           MA++ L ++ K+Y G   +  +I+LDIE GE +VFVGPSGCGKSTLLR+IAGLE IT G 
Sbjct: 1   MANLKLTNVEKTYAGAVNVLNNINLDIEKGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 60

Query: 60  LLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAE 119
           L ID Q VND+PP  R + MVFQSYALYPHMTV ENM+F LK+A   + EI   VE  A+
Sbjct: 61  LEIDGQVVNDMPPAMRGIAMVFQSYALYPHMTVRENMSFALKIAKKPQSEIDAAVERAAK 120

Query: 120 ILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARL 179
           +LQLD  L+R PK LSGGQRQRVAIGR++VR+PKV+LFDEPLSNLDA LRV  RIEIA+L
Sbjct: 121 MLQLDPYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRIEIAQL 180

Query: 180 HQRI-RSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQ 238
            +++  STMIYVTHDQVEAMTLA +IVVL    IAQVG PL LY  P + FVA F+GSP 
Sbjct: 181 KEQMPESTMIYVTHDQVEAMTLASRIVVLANKGIAQVGAPLELYERPNSEFVAQFIGSPS 240

Query: 239 MNFVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDEADFTF 298
           MN +    +    +T T+++  G         +    G  + +G+RPE FV     D  F
Sbjct: 241 MNLLPGEIVGTGQQT-TVKMDGGGVAVSDYPTTDADMGLKVNVGVRPEDFV-GTSGDHIF 298

Query: 299 HGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHLF 353
            G++ + E LG+  LLY   +     +   + G      G+T   G   DK H+F
Sbjct: 299 EGRVEITEALGEVTLLYFEKQGDGHAVIGKLPGIHAELRGKTVKLGASPDKVHIF 353


Lambda     K      H
   0.322    0.139    0.405 

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: 409
Number of extensions: 21
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: 371
Length of database: 362
Length adjustment: 30
Effective length of query: 341
Effective length of database: 332
Effective search space:   113212
Effective search space used:   113212
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 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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