GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylG in Dyella japonica UNC79MFTsu3.2

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2413
          Length = 505

 Score =  353 bits (906), Expect = e-102
 Identities = 200/497 (40%), Positives = 311/497 (62%), Gaps = 12/497 (2%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           +L+ + + KRF    AL GV +    GEVHA++G+NGAGKSTL+K++ GV +PD G +  
Sbjct: 12  VLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVEL 71

Query: 64  EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMG--DEEKRGIFIDYKKMYREA 121
           +GR +  + P EA   GI TV+QE+++  NLSVAEN++ G     +R   ID++++ R+ 
Sbjct: 72  DGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQV-RDG 130

Query: 122 EKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181
            + +  +  +E+D +  LG Y +AI+QMV IARA+   A+VLILDEPTSSL + E  +LF
Sbjct: 131 ARSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELF 190

Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241
            V+  L+E+G+AI+F++H L++++ + D+++VLRDG  +G  ++ +L    +V  MVGR 
Sbjct: 191 RVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMVGRD 250

Query: 242 LEKFYIKEAHE------PGEVVLEVKNLSGERFENVSFSLRRGEILGFAGLVGAGRTELM 295
           L      +A        P  +  +     G +   V   +RRGE+LG  GL+G+GRTEL 
Sbjct: 251 LPTVAGADAERAPPPDAPPAIDAQGLGCRG-KLHPVDLQVRRGEMLGLGGLLGSGRTELA 309

Query: 296 ETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPS 355
             +FG      GE+ I G+RVE+ HP DA+ +G+ L PE+RK  G++  +S+  N+ L +
Sbjct: 310 RLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVRENIVL-A 368

Query: 356 LDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKI 415
           L   +    +S  R+ ELA   ++   I+ A  +  V  LSGGNQQKV+LA+WL  +P++
Sbjct: 369 LQARQGWRGMSRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWLVTEPRL 428

Query: 416 LILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGI 475
           LILDEPTRGIDV AK E+   +++ A  G+ V+ IS+E  E+ +  DRIAVM   + AG 
Sbjct: 429 LILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERRKAGE 488

Query: 476 IDAKEASQEKVMKLAAG 492
           +    +++ +V+ + AG
Sbjct: 489 LPG-GSTEARVLAMIAG 504


Lambda     K      H
   0.318    0.138    0.385 

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: 610
Number of extensions: 26
Number of successful extensions: 8
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: 494
Length of database: 505
Length adjustment: 34
Effective length of query: 460
Effective length of database: 471
Effective search space:   216660
Effective search space used:   216660
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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