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

GapMind for catabolism of small carbon sources

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

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2413
          Length = 505

 Score =  350 bits (897), Expect = e-101
 Identities = 226/508 (44%), Positives = 303/508 (59%), Gaps = 20/508 (3%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72
           +L  R + K F    AL  V+L   AGEVHALMG+NGAGKSTL+K+L+G    D G    
Sbjct: 12  VLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGS-VE 70

Query: 73  IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGL-VARGDMVRAC 131
           +DG+ +    P  A+  G+  +YQE++L PNLSVAEN+Y GR  +RR L +     VR  
Sbjct: 71  LDGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDG 130

Query: 132 APTLAR-LGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190
           A +L R L  +    A + S  +A RQ+V IARA+   AR+L++DEPT+ L   E   LF
Sbjct: 131 ARSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELF 190

Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRD 250
            +I QLR  GMAIL+++H + ++  ++DR+TVLRDGC VG    A L  AALV  MVGRD
Sbjct: 191 RVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMVGRD 250

Query: 251 LSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDL--RAGEVLGLAGLVGAGRTELAR 308
           L         +A   +   ++     G R K    DL  R GE+LGL GL+G+GRTELAR
Sbjct: 251 LPTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGRTELAR 310

Query: 309 LVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHE 368
           L+FG D   RGE+RI      G  V L    P  A+  G+A   E+RK  G+  + SV E
Sbjct: 311 LLFGLDRAERGELRIG-----GERVELKH--PADAVVRGLALCPEERKTDGIVAELSVRE 363

Query: 369 NINLIVAARDAL-GLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSR 427
           NI L + AR    G+ R  +    R+  +A   LGI+ A  +  VG LSGGNQQKVML+R
Sbjct: 364 NIVLALQARQGWRGMSRARQDELARQLVQA---LGIKAADIETPVGLLSGGNQQKVMLAR 420

Query: 428 LLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVM 487
            L  +PR+LILDEPTRG+D+ AK E+   +   A +G+A+L IS+E  E+   CDR+ VM
Sbjct: 421 WLVTEPRLLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVM 480

Query: 488 REGTLAGEVRPAGSAAETQERIIALATG 515
           RE   AGE+ P GS   T+ R++A+  G
Sbjct: 481 RERRKAGEL-PGGS---TEARVLAMIAG 504


Lambda     K      H
   0.320    0.136    0.382 

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: 736
Number of extensions: 35
Number of successful extensions: 10
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: 540
Length of database: 505
Length adjustment: 35
Effective length of query: 505
Effective length of database: 470
Effective search space:   237350
Effective search space used:   237350
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources