GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16930 in Echinicola vietnamensis KMM 6221, DSM 17526

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component

Query= uniprot:B2SYR5
         (512 letters)



>FitnessBrowser__Cola:Echvi_1282
          Length = 502

 Score =  375 bits (964), Expect = e-108
 Identities = 205/501 (40%), Positives = 316/501 (63%), Gaps = 12/501 (2%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L   NI K F GV+ALD VS ++  G+V  ++GENGAGKSTL+KIL G Y    G +  +
Sbjct: 2   LTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYYN 61

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNS-LGWVNKREAKRFVRE 123
           G+ V+F +   +   GI +IHQEL  +P L++ EN+ LG+ P + +G ++  +  +   +
Sbjct: 62  GDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEAAQ 121

Query: 124 RLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLV 183
            L  + + +DP   + +L + Q+Q+VEI KAL   ++VI +DEPTS++S +E E+LF ++
Sbjct: 122 LLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGII 181

Query: 184 RDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREIS 243
           R LRA+ +A+ YISH++DE++ + D   + RDG+ I S   +EG+T + ++ +MVGREI 
Sbjct: 182 RALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIES-GEMEGMTEEALIQKMVGREIV 240

Query: 244 DIYNYSARPLGEVRFAAK-------GIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELM 296
              + S R   E   + K        I    L Q  +FE+ +GE++G FGL+GAGR+ELM
Sbjct: 241 IERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTELM 300

Query: 297 HLVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISC 356
             ++G    +G E+ L GK  + +   EA+  G+ L PEDRK++G+V    +  N +++ 
Sbjct: 301 EALFGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSSLTV 360

Query: 357 RRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDL 416
               L  G+ LD KKE   A +++  LKIK  S RQ +  LSGGNQQK +L++WLA    
Sbjct: 361 VDSILSGGL-LDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWLATRP- 418

Query: 417 KVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRIS 476
           KV++LDEPTRGID+ AK+EIY +I QLA  G  ++++SSELPE+L VSDR++VM +GR++
Sbjct: 419 KVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEGRLT 478

Query: 477 GEL-TRKDATEQSVLSLALPQ 496
             +      +E  +L  A+P+
Sbjct: 479 ANIPIDAQTSEDEILQAAIPK 499



 Score = 77.8 bits (190), Expect = 9e-19
 Identities = 53/228 (23%), Positives = 106/228 (46%), Gaps = 6/228 (2%)

Query: 20  LDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMIDGNEVRFTSAASSIAA 79
           L  ++F++  G+V G+ G  GAG++ L++ L G        + + G    F     ++ A
Sbjct: 273 LQDINFELGKGEVLGIFGLMGAGRTELMEALFGVLPHQGAEITLAGKVHEFQKPQEAMDA 332

Query: 80  GIAVIHQE-----LQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRERLEAMGVALDP 134
           G+A++ ++     L    DL    +L +     S G ++ ++ K   ++ +  + +    
Sbjct: 333 GLALVPEDRKQDGLVLCMDLCTNSSLTVVDSILSGGLLDDKKEKGLAQKYMGELKIKASS 392

Query: 135 NAKL-RKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVRDLRADNRAM 193
           + +L  KLS   +Q V + K L    +V+ LDEPT  +       ++KL+R L  +   +
Sbjct: 393 HRQLVEKLSGGNQQKVVLAKWLATRPKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGL 452

Query: 194 IYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGRE 241
           I +S  + EI  + D   +  +GR  A+ P     + D I+   + ++
Sbjct: 453 IVVSSELPEILAVSDRVLVMAEGRLTANIPIDAQTSEDEILQAAIPKK 500


Lambda     K      H
   0.320    0.136    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: 666
Number of extensions: 41
Number of successful extensions: 10
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: 512
Length of database: 502
Length adjustment: 34
Effective length of query: 478
Effective length of database: 468
Effective search space:   223704
Effective search space used:   223704
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