GapMind for catabolism of small carbon sources

 

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

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__Cola:Echvi_1282
          Length = 502

 Score =  394 bits (1012), Expect = e-114
 Identities = 220/501 (43%), Positives = 330/501 (65%), Gaps = 8/501 (1%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           +L ++NITK F GVKAL++V+L+++ G + A++GENGAGKSTLMK+LSGVYP   Y+G I
Sbjct: 1   MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYP--DYKGTI 58

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQTFNR 123
           +Y G    F+   D+++ GI IIHQEL L+P LSI ENIFLG E  +  G++   +    
Sbjct: 59  YYNGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKE 118

Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183
             +LL ++ L   PET ++ + VG+QQLVEIAKALS   +++I+DEPT+++++ + E L 
Sbjct: 119 AAQLLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILF 178

Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243
            ++   R +G     I+HKL+E+  +AD+  VLRDG  +++ +   E ++E+ +I+ MVG
Sbjct: 179 GIIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGE--MEGMTEEALIQKMVG 236

Query: 244 RDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303
           R++            ET+L VK+    H +  D+ +L DIN  + KGEV+GI GLMGAGR
Sbjct: 237 REIVIERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGR 296

Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363
           TE   ++FG    H+   ++ + GK  +    ++A+DAGLA V EDRK  GLVL  ++  
Sbjct: 297 TELMEALFGV-LPHQ-GAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCT 354

Query: 364 NTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423
           N++L  +  +    ++DD KE  +A  +   L+I++S   Q    LSGGNQQKVVL+KWL
Sbjct: 355 NSSLTVVDSILSGGLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWL 414

Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483
            + P VL+LDEPTRGID+ AK EIY +I QLA +G G++++SSE+PE+L   DR+ VM E
Sbjct: 415 ATRPKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAE 474

Query: 484 GRIVAELP-KGEASQESIMRA 503
           GR+ A +P   + S++ I++A
Sbjct: 475 GRLTANIPIDAQTSEDEILQA 495



 Score = 72.0 bits (175), Expect = 5e-17
 Identities = 59/230 (25%), Positives = 109/230 (47%), Gaps = 11/230 (4%)

Query: 278 QVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRK 337
           + L D+++ ++ G V  I G  GAG++     + G    ++  G +  +G PV     R 
Sbjct: 15  KALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYK--GTIYYNGDPVKFQNTRD 72

Query: 338 AIDAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRI 397
           A + G+  + ++   L L+   +I  N  L      +   ++D  K  K A+    RL++
Sbjct: 73  AQEKGINIIHQE---LNLIPYLSIRENIFLGR-EPETPMGLLDVAKMHKEAAQLLHRLKL 128

Query: 398 RSSGIFQETV--NLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLA 455
               +  ET    L  G QQ V ++K L     V+I+DEPT  I       ++ II  L 
Sbjct: 129 N---VDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGIIRALR 185

Query: 456 ADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505
           A+GK +  IS ++ EL    DR  V+ +G+++        ++E++++ ++
Sbjct: 186 AEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMV 235


Lambda     K      H
   0.316    0.135    0.374 

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: 645
Number of extensions: 38
Number of successful extensions: 8
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

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

Links

Downloads

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:

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