GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gatA in Escherichia coli BW25113

Align The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized)
to candidate 18059 b4031 D-xylose transporter (NCBI)

Query= TCDB::A2R3H2
         (518 letters)



>FitnessBrowser__Keio:18059
          Length = 491

 Score =  198 bits (504), Expect = 3e-55
 Identities = 144/502 (28%), Positives = 240/502 (47%), Gaps = 66/502 (13%)

Query: 9   VYLLTAVAYSGSLLFGYDTGVM-GSVLSLTSFKEDFGIPTGSSGFASSKSSEISSNVVSL 67
           ++ +T VA  G LLFGYDT V+ G+V SL +      +       + S ++ +    V+ 
Sbjct: 10  IFSITLVATLGGLLFGYDTAVISGTVESLNT------VFVAPQNLSESAANSLLGFCVAS 63

Query: 68  LTAGCFFGAIFAAPLNERIGRRYALMIFTVIFLIGAA-----------------VQVASK 110
              GC  G       + R GRR +L I  V+F I                    V V   
Sbjct: 64  ALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLA 123

Query: 111 HHIGQIYGGRVIAGLGIGGMSSITPVFVSENCPPSIRGRVAGMFQEFLVIGSTFAYWLDY 170
            ++ +    R+I G+G+G  S ++P++++E  P  IRG++    Q  ++ G    Y ++Y
Sbjct: 124 GYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNY 183

Query: 171 GVSLHIPSS---TKQWRVPVAVQLIPGGLMLLGLFFLKESPRWLAGKGRHEEALQSLAYI 227
            ++    +S   T  WR   A + IP  L L+ L+ + ESPRWL  +G+ E+A   L  I
Sbjct: 184 FIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKI 243

Query: 228 RNESPDSEEIQKEFAEIRAAIDEEVAATEGLTYKEFIQPSNLKRFG-----FAFTLMLSQ 282
              +  ++ +Q    EI+ ++D     T G           L  FG         L + Q
Sbjct: 244 MGNTLATQAVQ----EIKHSLDHG-RKTGG----------RLLMFGVGVIVIGVMLSIFQ 288

Query: 283 QFTGTNSIGYYAPEIFQTIGLSATNSSLFATGVYGTVKVVATAIFLFVGIDRWGRKLSLV 342
           QF G N + YYAPE+F+T+G S T+ +L  T + G + +  T + +   +D++GRK   +
Sbjct: 289 QFVGINVVLYYAPEVFKTLGAS-TDIALLQTIIVGVINLTFTVLAIMT-VDKFGRKPLQI 346

Query: 343 GGSIWMASMMFIIGAVLATHPPDTSASGVSQASIAMVVMIYLYVIGYSASWGPTPWVYVS 402
            G++ MA  MF +G    T  P           +A++ M++ YV  ++ SWGP  WV +S
Sbjct: 347 IGALGMAIGMFSLGTAFYTQAPGI---------VALLSMLF-YVAAFAMSWGPVCWVLLS 396

Query: 403 EIFPTRLRSYGVGLAATSQWLWSFVVTEITPK-------AVHNIGWRTFLMFGIFCVAMC 455
           EIFP  +R   + +A  +QWL ++ V+   P          H     ++ ++G   V   
Sbjct: 397 EIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAA 456

Query: 456 VFVIVFAKETKGRSLEDMDILF 477
           +F+  F  ETKG++LE+++ L+
Sbjct: 457 LFMWKFVPETKGKTLEELEALW 478


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: 606
Number of extensions: 38
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: 518
Length of database: 491
Length adjustment: 34
Effective length of query: 484
Effective length of database: 457
Effective search space:   221188
Effective search space used:   221188
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