GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34245 in Echinicola vietnamensis KMM 6221, DSM 17526

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__Cola:Echvi_1282
          Length = 502

 Score =  272 bits (695), Expect = 2e-77
 Identities = 167/479 (34%), Positives = 263/479 (54%), Gaps = 11/479 (2%)

Query: 20  VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAP 79
           +TK F    AL+DVS+ +  G   A++G NGAGKSTL+ IL+G+     G + ++G    
Sbjct: 7   ITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYYNGDPVK 66

Query: 80  SIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRG-GVIDWQAMRRDARALLDHW 138
               RDA  + +  ++Q   +I  LS+ EN+F+ R+P    G++D   M ++A  LL   
Sbjct: 67  FQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEAAQLLHRL 126

Query: 139 KIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQR 198
           K++V  +     L V  +QLVEIA+ALS  ++ II+DEPT+ +   E++ LF  I  L+ 
Sbjct: 127 KLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGIIRALRA 186

Query: 199 EGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGLAVADA 258
           EG    +ISH L E++ I     VLRD + I S  +  +  E LI+ M G      V + 
Sbjct: 187 EGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGRE---IVIER 243

Query: 259 AARGALPADTAVA---LELKELTGAD---YEGVSFTVKRGEVVGLTGATSSGRTSVAEAI 312
           +  G    +T ++   L +K    AD    + ++F + +GEV+G+ G   +GRT + EA+
Sbjct: 244 SCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTELMEAL 303

Query: 313 AGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARV 372
            G+   +   I++ G +        ++  G+  VP+DR  +GLVL   +  N+S+T+   
Sbjct: 304 FGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSSLTVVDS 363

Query: 373 LGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVL 432
           +   G+    K+    QK +  L I A     +V  LSGGNQQKVV+A+ LAT P VL+L
Sbjct: 364 ILSGGLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWLATRPKVLML 423

Query: 433 IDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRVAAEFP 490
            +PT G+D+ +K  +  ++ ++  EG  ++VVS EL + L   DRVLVM  GR+ A  P
Sbjct: 424 DEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEGRLTANIP 482



 Score = 65.5 bits (158), Expect = 4e-15
 Identities = 52/220 (23%), Positives = 99/220 (45%), Gaps = 6/220 (2%)

Query: 30  LNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIADRDAWRE 89
           L D++  +  GE   + G  GAG++ L+  L G+      E+  +G        ++A   
Sbjct: 273 LQDINFELGKGEVLGIFGLMGAGRTELMEALFGVLPHQGAEITLAGKVHEFQKPQEAMDA 332

Query: 90  RVACVYQHS-----TIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARALLDHWKIDVRE 144
            +A V +        +  DL    +L +    L GG++D +  +  A+  +   KI    
Sbjct: 333 GLALVPEDRKQDGLVLCMDLCTNSSLTVVDSILSGGLLDDKKEKGLAQKYMGELKIKASS 392

Query: 145 DARAGD-LSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQREGVTF 203
             +  + LS   +Q V +A+ L+   + ++LDEPT  +D +    +++ I +L  EG+  
Sbjct: 393 HRQLVEKLSGGNQQKVVLAKWLATRPKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGL 452

Query: 204 LFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLI 243
           + +S  L E+  +   V V+ + R   + P+ A   E  I
Sbjct: 453 IVVSSELPEILAVSDRVLVMAEGRLTANIPIDAQTSEDEI 492


Lambda     K      H
   0.318    0.134    0.377 

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: 508
Number of extensions: 31
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 510
Length of database: 502
Length adjustment: 34
Effective length of query: 476
Effective length of database: 468
Effective search space:   222768
Effective search space used:   222768
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.

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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