GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Klebsiella michiganensis M5al

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__Koxy:BWI76_RS14860
          Length = 510

 Score =  410 bits (1054), Expect = e-119
 Identities = 248/513 (48%), Positives = 330/513 (64%), Gaps = 17/513 (3%)

Query: 4   MSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAY 63
           M+D S+  PLL L  I K +    AL  V    +AGEVHALMGENGAGKSTLMKILSG  
Sbjct: 1   MADISSP-PLLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNE 59

Query: 64  TADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRA-LQRRGLV 122
             D  G   IDGQ + I  P+ AR  G+A+I+QEL+  P+++VAEN++LG+      G++
Sbjct: 60  QRD-SGVIFIDGQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGIL 118

Query: 123 ARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLS 182
            R  M R     L R+ AD  P A + SLSI ++Q+VEIARAV   A++LV+DEPT  LS
Sbjct: 119 DRKRMHREAKEKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALS 178

Query: 183 THETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAAL 242
             ET +L+ LI Q+R +G+ ++YISHRM E+ +LA+RVTV RDG ++GT +  ++S   +
Sbjct: 179 RAETLQLYRLIAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDI 238

Query: 243 VKMMVGRDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAG 302
           V+MMVGR +   Y   H      +V+L VRD+A G      SF++ AGEV+ ++GLVG+G
Sbjct: 239 VRMMVGRQIVDLY--QHEPRTPGDVLLEVRDLA-GSATGPVSFEVSAGEVVSMSGLVGSG 295

Query: 303 RTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFL 362
           RTE+ARL+FGAD R++G VR+A      G  + P+  P  AI  GI  +TEDRK QGLFL
Sbjct: 296 RTEVARLLFGADPRSQGSVRLA------GRESQPS-DPTAAIADGIGMVTEDRKTQGLFL 348

Query: 363 DQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQK 422
             SV  NI++        G G + R   R    E +  L +R    ++ V ALSGGNQQK
Sbjct: 349 GHSVEHNIDISSLDNFVAG-GVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQK 407

Query: 423 VMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCD 482
             L+R L    R+LILDEPTRGVDIGAK EIY LI+ LA++G AIL+ISS+LPE +G+ D
Sbjct: 408 AALARWLLRDSRLLILDEPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISD 467

Query: 483 RVLVMREGTLAGEVRPAGSAAETQERIIALATG 515
           RVLVMR G +   V    S + T+E ++  ATG
Sbjct: 468 RVLVMRGGRI---VHQLPSCSATEEEVMLHATG 497


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: 660
Number of extensions: 36
Number of successful extensions: 9
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: 510
Length adjustment: 35
Effective length of query: 505
Effective length of database: 475
Effective search space:   239875
Effective search space used:   239875
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