GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gatA in Klebsiella michiganensis M5al

Align The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized)
to candidate BWI76_RS24055 BWI76_RS24055 MFS transporter

Query= TCDB::A2R3H2
         (518 letters)



>FitnessBrowser__Koxy:BWI76_RS24055
          Length = 464

 Score =  200 bits (509), Expect = 8e-56
 Identities = 146/468 (31%), Positives = 241/468 (51%), Gaps = 38/468 (8%)

Query: 10  YLLTAVAYSGSLLFGYDTGVMGSVLSLTSFKEDFGIPTGSSGFASSKSSEISSNVVSLLT 69
           + +  +A    LLFG D GV+   L   +   +F I           S+     VVS + 
Sbjct: 16  FFVCFLAALAGLLFGLDIGVIAGALPFIA--NEFQI-----------SAHTQEWVVSSMM 62

Query: 70  AGCFFGAIFAAPLNERIGRRYALMIFTVIFLIGAAVQVASKHHIGQIYGGRVIAGLGIGG 129
            G   GA+ +  L+ ++GR+ +LMI  ++F+ G+    A+ + +  +   RV+ GL +G 
Sbjct: 63  FGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPN-VEVLLISRVLLGLAVGV 121

Query: 130 MSSITPVFVSENCPPSIRGRVAGMFQEFLVIGSTFAYWLDYGVSLHIPSSTKQWRVPVAV 189
            S   P+++SE  P  IRG +  M+Q  + IG   AY  D   S      +  WR  + V
Sbjct: 122 ASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSY-----SGAWRWMLGV 176

Query: 190 QLIPGGLMLLGLFFLKESPRWLAGKGRHEEALQSLAYIRNESPDSEEIQKEFAEIRAAID 249
            +IP  L+L+G+ FL +SPRW A K R  +A + L  +R+    S E ++E  EIR ++ 
Sbjct: 177 IIIPAVLLLIGVVFLPDSPRWFAAKRRFVDAERVLLRLRD---TSAEAKRELDEIRESLK 233

Query: 250 EEVAATEGLTYKEFIQPSNLKRFGF-AFTLMLSQQFTGTNSIGYYAPEIFQTIGLSATNS 308
            + +      +  F + SN +R  F    L + QQFTG N I YYAP+IF+  G + T  
Sbjct: 234 VKQSG-----WSLFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYANTTE 288

Query: 309 SLFATGVYGTVKVVATAIFLFVG-IDRWGRKLSLVGGSIWMASMMFIIGAVLATHPPDTS 367
            ++ T + G   V+AT  F+ +G +DRWGRK +L+ G I MA  M I+G+++  H    S
Sbjct: 289 QMWGTVIVGLTNVLAT--FIAIGLVDRWGRKPTLILGFIVMALGMGILGSMM--HIGIHS 344

Query: 368 ASGVSQASIAMVVMIYLYVIGYSASWGPTPWVYVSEIFPTRLRSYGVGLAATSQWLWSFV 427
           A+    A    V+M+ ++++G++ S GP  WV  SEI P + R +G+  +  + W+ + +
Sbjct: 345 AT----AQYFAVLMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMI 400

Query: 428 VTEITPKAVHNIG-WRTFLMFGIFCVAMCVFVIVFAKETKGRSLEDMD 474
           V       ++++G   TF ++G   +      +    ETK  SLE ++
Sbjct: 401 VGATFLTMLNSLGSANTFWVYGGLNILFIFLTLWLIPETKNVSLEHIE 448


Lambda     K      H
   0.323    0.137    0.411 

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: 613
Number of extensions: 36
Number of successful extensions: 7
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: 518
Length of database: 464
Length adjustment: 34
Effective length of query: 484
Effective length of database: 430
Effective search space:   208120
Effective search space used:   208120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 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