GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate WP_085638891.1 MGEO_RS13900 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039
         (367 letters)



>NCBI__GCF_002115805.1:WP_085638891.1
          Length = 362

 Score =  320 bits (821), Expect = 3e-92
 Identities = 170/355 (47%), Positives = 244/355 (68%), Gaps = 5/355 (1%)

Query: 1   MANLKIKNLQKGFEG-FSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGT 59
           MANLK+ N++K + G  +++  I+L++   E +VFVGPSGCGKSTLLR+IAGLE+++GGT
Sbjct: 1   MANLKLTNVEKTYAGAVNVLNNINLDIEKGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 60

Query: 60  IELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAAR 119
           +E+DG+ + ++ PA R +AMVFQ+YALYPHM+VR+NMSFAL +A   ++E++  V  AA+
Sbjct: 61  LEIDGQVVNDMPPAMRGIAMVFQSYALYPHMTVRENMSFALKIAKKPQSEIDAAVERAAK 120

Query: 120 ILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRL 179
           +L+L P L+R PK LSGGQRQRVAIGR+IVR+PK++LFDEPLSNLDAALRV  R+E+ +L
Sbjct: 121 MLQLDPYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRIEIAQL 180

Query: 180 HKEL-QATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPK 238
            +++ ++TMIYVTHDQVEAMT+A ++VVL    I QVG+PL+LY +P + FVA F+G+P 
Sbjct: 181 KEQMPESTMIYVTHDQVEAMTLASRIVVLANKGIAQVGAPLELYERPNSEFVAQFIGSPS 240

Query: 239 MGFLKGKITRVDSQGCEVQLDAGTRVSLPLGGRHLSVGSAVTLGIRPEHLELAKPGDCAL 298
           M  L G+I     Q   V++D G             +G  V +G+RPE   +   GD   
Sbjct: 241 MNLLPGEIVGTGQQ-TTVKMDGGGVAVSDYPTTDADMGLKVNVGVRPEDF-VGTSGDHIF 298

Query: 299 QVTADVSERLGSDTFCHV-RTASGEALTMRVRGDLASRYGETLSLHLDAQHCHLF 352
           +   +++E LG  T  +  +   G A+  ++ G  A   G+T+ L       H+F
Sbjct: 299 EGRVEITEALGEVTLLYFEKQGDGHAVIGKLPGIHAELRGKTVKLGASPDKVHIF 353


Lambda     K      H
   0.320    0.137    0.389 

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: 400
Number of extensions: 19
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: 367
Length of database: 362
Length adjustment: 29
Effective length of query: 338
Effective length of database: 333
Effective search space:   112554
Effective search space used:   112554
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: 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