GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Echinicola vietnamensis KMM 6221, DSM 17526

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__Cola:Echvi_1282
          Length = 502

 Score =  340 bits (871), Expect = 1e-97
 Identities = 204/492 (41%), Positives = 300/492 (60%), Gaps = 19/492 (3%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72
           +L ++NI K F GV+AL  V L   AG V A++GENGAGKSTLMKILSG Y  D  G  +
Sbjct: 1   MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYP-DYKGTIY 59

Query: 73  IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQR-RGLVARGDMVRAC 131
            +G  V+    + A++ G+ +I+QEL+L P LS+ ENI+LGR  +   GL+    M +  
Sbjct: 60  YNGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEA 119

Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191
           A  L RL  +  P   V+ L + Q+QLVEIA+A+  E+++++MDEPT+ +S  E + LF 
Sbjct: 120 AQLLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFG 179

Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251
           +IR LR EG AI YISH++ E+  +ADR  VLRDG  + + +   +++ AL++ MVGR++
Sbjct: 180 IIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGREI 239

Query: 252 SGFYTKTHGQAVEREVMLSVR-------DVADGRRVKGCSFDLRAGEVLGLAGLVGAGRT 304
                   G+  + E +LSV+        +AD   ++  +F+L  GEVLG+ GL+GAGRT
Sbjct: 240 V-IERSCSGRQFD-ETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRT 297

Query: 305 ELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQ 364
           EL   +FG       E+ +A               P++A+DAG+A + EDRK  GL L  
Sbjct: 298 ELMEALFGVLPHQGAEITLAGKVHE-------FQKPQEAMDAGLALVPEDRKQDGLVLCM 350

Query: 365 SVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVM 424
            +  N +L V     L  G L+    +    + +  L I+ +  +  V  LSGGNQQKV+
Sbjct: 351 DLCTNSSLTV-VDSILSGGLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVV 409

Query: 425 LSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRV 484
           L++ L  +P+VL+LDEPTRG+DI AK+EIY+LI  LA  G+ ++++SSELPE++ + DRV
Sbjct: 410 LAKWLATRPKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRV 469

Query: 485 LVMREGTLAGEV 496
           LVM EG L   +
Sbjct: 470 LVMAEGRLTANI 481


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: 552
Number of extensions: 30
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: 502
Length adjustment: 35
Effective length of query: 505
Effective length of database: 467
Effective search space:   235835
Effective search space used:   235835
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.

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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