Aligments for a candidate for H281DRAFT_01113 in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Aligments for a candidate for H281DRAFT_01113 in Echinicola vietnamensis KMM 6221, DSM 17526

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>FitnessBrowser__Cola:Echvi_1282
          Length = 502

 Score =  312 bits (799), Expect = 2e-89
 Identities = 183/504 (36%), Positives = 296/504 (58%), Gaps = 16/504 (3%)

Query: 16  LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75
           L V  + K F GV AL  VSL  Q G++  +LGENG GKSTL+KI+SG  P  +G +   
Sbjct: 2   LTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYYN 61

Query: 76  GVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAA 135
           G P    +  +A   GI  ++Q+L+L+P +S+ EN+ L  E  T  G L    D   +  
Sbjct: 62  GDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLL----DVAKMHK 117

Query: 136 TAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 195
            AA+ L  + L  + E   T + QL +  +QLV IA+A++ E++ +IMDEPT++++ +EV
Sbjct: 118 EAAQLLHRLKLNVDPE---TPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEV 174

Query: 196 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELM 255
           + L  ++  LRA+G  + ++SHKLDE +AI    +VLRDG+ +  G +   T+  + + M
Sbjct: 175 EILFGIIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKM 234

Query: 256 TGRHLSNERYRESAHAQDIVLDVRGFTR-----AGQF--SDVSFKLHGGEILGVTGLLDS 308
            GR +  ER        + VL V+  T      A +F   D++F+L  GE+LG+ GL+ +
Sbjct: 235 VGREIVIERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGA 294

Query: 309 GRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRD 368
           GR EL  AL GV P Q  ++ L G+    + P +A    +  VPEDR  +GL L   +  
Sbjct: 295 GRTELMEALFGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCT 354

Query: 369 NVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRW 428
           N    ++ S+    G +D  + + LA++ + EL+I      + V+ LSGGNQQ+V++ +W
Sbjct: 355 NSSLTVVDSILSG-GLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKW 413

Query: 429 LAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMK 488
           LA  P+VL+L  PT G+D+ +K+ IY+++++L+  G+G+I++S +LPE+L   DR+L+M 
Sbjct: 414 LATRPKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMA 473

Query: 489 KGHVSAEYRAD-ELSEADLYHALL 511
           +G ++A    D + SE ++  A +
Sbjct: 474 EGRLTANIPIDAQTSEDEILQAAI 497


Lambda     K      H
   0.319    0.135    0.376 

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: 549
Number of extensions: 29
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: 515
Length of database: 502
Length adjustment: 34
Effective length of query: 481
Effective length of database: 468
Effective search space:   225108
Effective search space used:   225108
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 (21.7 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

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, or view the source code.

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