GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Halomonas xinjiangensis TRM 0175

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

Query= reanno::acidovorax_3H11:Ac3H11_791
         (363 letters)



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  173 bits (439), Expect = 6e-48
 Identities = 119/337 (35%), Positives = 181/337 (53%), Gaps = 15/337 (4%)

Query: 21  MSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVDGKDVTGMPVRDRNVAMVY 80
           + L +  G   VL+G +  GK++L+R++AGL+  T G + +D + V  +   +R++AMV+
Sbjct: 23  IDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGTLKIDDRVVNDLEPAERDIAMVF 82

Query: 81  QQFINYPSMKVAANIASPLKLRGEKN--IDARVREIASRLHIDMFLDRYPAELSGGQQQR 138
           Q +  YP M V  N+A  LK RG K   I+ RV + A+ L I+ FL+R P +LSGGQ+QR
Sbjct: 83  QNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAAMLEIEPFLERKPRKLSGGQRQR 142

Query: 139 VALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAGQSTVVYATTEPGEALLLG 198
           VA+ RAL +     L DEPL NLD KLR ++R E+ QL    ++T +Y T +  EAL LG
Sbjct: 143 VAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQLQRRLKTTSLYVTHDQLEALTLG 202

Query: 199 GYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMAASATAQGVRLQGGAELTL 258
               VL+ G + Q G   EV+  P S+ VA     P MN++  +     +R +G   L  
Sbjct: 203 DRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPAMNMLPVAY----LRERGANGLLD 258

Query: 259 PLPQGAATAAGLTVGVRASALRVHARPGD-VSVAGVVELAEISGSDTFVHASTPWGD--L 315
            L      A    +G+R   LR+ A   D + V G VEL E +G+++ ++ S    D   
Sbjct: 259 HL-----AADTDVIGIRPDDLRIEAPDEDHLVVTGTVELFEAAGAESHLYVSLEGSDQPT 313

Query: 316 VAQLTGVHYFELGTAITLHLDPAQAYVFG-ADGRLAQ 351
           V + +       G  +  H+ P+  + F  A G+  Q
Sbjct: 314 VIRTSARPPVAEGETMRFHVLPSALHPFNQASGKRTQ 350


Lambda     K      H
   0.318    0.133    0.375 

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: 251
Number of extensions: 10
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: 363
Length of database: 354
Length adjustment: 29
Effective length of query: 334
Effective length of database: 325
Effective search space:   108550
Effective search space used:   108550
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: 41 (21.7 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