GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Halomonas xinjiangensis TRM 0175

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= reanno::Smeli:SMc03065
         (362 letters)



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  334 bits (857), Expect = 2e-96
 Identities = 179/357 (50%), Positives = 242/357 (67%), Gaps = 18/357 (5%)

Query: 1   MTGLLLKDIRKSY-GAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGD 59
           M  + L  ++K+Y G V+ + GIDL+I +GEFVV VGPSGCGKSTLLRM+AGLE IT G 
Sbjct: 1   MASIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGT 60

Query: 60  MFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAAD 119
           + ID   VND+ P++R IAMVFQ+YALYPHMTV+ N+A+G++     +EEI+RRV  AA 
Sbjct: 61  LKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAA 120

Query: 120 MLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKL 179
           ML++ P+L+R P+ LSGGQRQRVA+GRA+ R P  FLFDEPLSNLDA LRV  R+EI +L
Sbjct: 121 MLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQL 180

Query: 180 SERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPA 239
             R+  TT +YVTHDQ+EA+TL DR+VVL+ G IEQVG P+E+YE+PA++FVA FIGSPA
Sbjct: 181 QRRLK-TTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPA 239

Query: 240 MNVIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRV--TEADDFL 297
           MN++P  +    ++ A  L    +   DV             G+RP+DLR+   + D  +
Sbjct: 240 MNMLP--VAYLRERGANGLLDHLAADTDV------------IGIRPDDLRIEAPDEDHLV 285

Query: 298 FEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFD 354
             GTV + EA G  + LY+     ++P + +      V  G+ +RF    + LH F+
Sbjct: 286 VTGTVELFEAAGAESHLYVSLEGSDQPTVIRTSARPPVAEGETMRFHVLPSALHPFN 342


Lambda     K      H
   0.320    0.137    0.387 

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: 354
Number of extensions: 9
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: 362
Length of database: 354
Length adjustment: 29
Effective length of query: 333
Effective length of database: 325
Effective search space:   108225
Effective search space used:   108225
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.

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