GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gatY in Herbaspirillum seropedicae SmR1

Align D-tagatose-1,6-bisphosphate aldolase subunit GatY; TBPA; TagBP aldolase; D-tagatose-bisphosphate aldolase class II; Tagatose-bisphosphate aldolase; EC 4.1.2.40 (characterized)
to candidate HSERO_RS03355 HSERO_RS03355 fructose-bisphosphate aldolase

Query= SwissProt::P0C8J6
         (284 letters)



>FitnessBrowser__HerbieS:HSERO_RS03355
          Length = 354

 Score =  172 bits (436), Expect = 1e-47
 Identities = 115/329 (34%), Positives = 174/329 (52%), Gaps = 45/329 (13%)

Query: 1   MYVVSTKQMLNNAQRGGYAVPAFNIHNLETMQVVVETAANLHAPVIIAGTPGTFTHAGTE 60
           M +VS +Q+L++A   GY +PAFN++NLE +  ++E A  + APVI+  + G   +AG  
Sbjct: 1   MPLVSMRQLLDHAAENGYGLPAFNVNNLEQVTAIMEAANEVGAPVIMQASAGARKYAGEA 60

Query: 61  NLLALVSAMAKQYHH-PLAIHLDHHTKFDDIAQKVRSGVRSVMIDASH-------LPFAQ 112
            L  L+SA  + Y H P+ +H DH          ++SG  SVM+D S          +  
Sbjct: 61  FLRHLISAAVEAYPHIPVVMHQDHGQSPAVCMAAIKSGFSSVMMDGSLEADGKTVASYEY 120

Query: 113 NISRVKEVVDFCHRFDVSVEAELGQLGGQE----DDVQVNEADA------LYTNPAQARE 162
           N+   ++VV+F H   V+VEAELG LG  E    D    + AD       L T+  QA +
Sbjct: 121 NVEVSRKVVEFSHAIGVTVEAELGVLGSLETMKGDKEDGHGADGTMTREQLLTDVNQAAD 180

Query: 163 FAEATGIDSLAVAIGTAHGMY--ASAPALDFSRLENIRQW----VNLPLVLHGAS----- 211
           F +AT  D+LA+AIGT+HG Y  +  P  D   ++ I++      N  LV+HG+S     
Sbjct: 181 FVKATQCDALAIAIGTSHGAYKFSRKPTGDILAIDRIKEIHARIPNTHLVMHGSSSVPQE 240

Query: 212 ----------------GLSTKDIQQTIKLGICKINVATELKNAFSQALKNYLTEHPEATD 255
                           G+  ++IQ+ IK G+ KIN+ T+++ A + A++ YL E+P   D
Sbjct: 241 LLAEIREFGGDMKETYGVPVEEIQEGIKHGVRKINIDTDIRLAMTGAIRRYLFENPSKFD 300

Query: 256 PRDYLQSAKSAMRDVVSKVIADCGCEGRA 284
           PRDYL+ A+ A + V        GCEG+A
Sbjct: 301 PRDYLKPAREAAKLVCKARFLSFGCEGQA 329


Lambda     K      H
   0.318    0.131    0.376 

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: 226
Number of extensions: 16
Number of successful extensions: 4
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: 284
Length of database: 354
Length adjustment: 27
Effective length of query: 257
Effective length of database: 327
Effective search space:    84039
Effective search space used:    84039
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 (21.7 bits)
S2: 48 (23.1 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