GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Cupriavidus basilensis 4G11

Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate RR42_RS13790 RR42_RS13790 ABC transporter

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



>FitnessBrowser__Cup4G11:RR42_RS13790
          Length = 366

 Score =  484 bits (1245), Expect = e-141
 Identities = 254/357 (71%), Positives = 288/357 (80%), Gaps = 2/357 (0%)

Query: 1   MQLALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVT 60
           MQL L+ I+++ G+Q +LY MSL    GAVT+LLGATQAGKTSLMR+MAGLD P+AGRV 
Sbjct: 1   MQLRLEGIAQQAGSQAYLYPMSLTPVPGAVTILLGATQAGKTSLMRVMAGLDRPSAGRVE 60

Query: 61  VDGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKNIDARVREIASRLHI 120
           VDG DVTGMPVR+RNV+MVYQQFINYPSM V  NIASPLKLR  ++ID +VR +A+RLHI
Sbjct: 61  VDGIDVTGMPVRERNVSMVYQQFINYPSMTVFDNIASPLKLRRSRDIDGQVRALATRLHI 120

Query: 121 DMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAG 180
           +  L+R+PAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFA G
Sbjct: 121 EHLLERFPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAHG 180

Query: 181 QSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMA 240
            +TV+YATTEP EALLLGGYTAVLD G+LLQYGPT EVFH P SLRVARAFSDPPMNLMA
Sbjct: 181 NATVIYATTEPAEALLLGGYTAVLDAGELLQYGPTPEVFHYPASLRVARAFSDPPMNLMA 240

Query: 241 ASATAQGVRLQGGAELTLPLPQGAATAAGLTVGVRASALRVHARPGDVSVAGVVELAEIS 300
            +  A  V L GG  + +PLP        +TVGVRA ALR+ A PG V VAG V LAE+S
Sbjct: 241 GNLLAGAVTLPGG--VVVPLPGAVEQGGTVTVGVRAGALRLDAVPGSVPVAGRVALAELS 298

Query: 301 GSDTFVHASTPWGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGADGRLAQAPARPV 357
           GSDTFVH  +P G+LVAQ  GV   ELG  +TLHLDPAQ Y+F ADG    AP+RP+
Sbjct: 299 GSDTFVHMDSPVGNLVAQFPGVVDLELGAPLTLHLDPAQLYLFDADGMRIHAPSRPL 355


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: 477
Number of extensions: 14
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: 366
Length adjustment: 29
Effective length of query: 334
Effective length of database: 337
Effective search space:   112558
Effective search space used:   112558
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 17 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