GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pgmA in Azospirillum brasilense Sp245

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate AZOBR_RS02670 AZOBR_RS02670 phosphoglucomutase

Query= BRENDA::Q9SCY0
         (623 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS02670 AZOBR_RS02670
           phosphoglucomutase
          Length = 543

 Score =  608 bits (1568), Expect = e-178
 Identities = 305/551 (55%), Positives = 401/551 (72%), Gaps = 14/551 (2%)

Query: 73  PTKPIEGQKTGTSGLRKKVKVFMEDNYLANWIQALFNSLPLEDYKNATLVLGGDGRYFNK 132
           PT P +GQK GTSGLRK VKVF +  YL N++Q++F+ +  +    ATLV+GGDGRY N+
Sbjct: 7   PTTPFDGQKPGTSGLRKAVKVFEQPRYLENFVQSIFDCV--DGLSGATLVIGGDGRYHNR 64

Query: 133 EASQIIIKIAAGNGVGQILVGKEGILSTPAVSAVIRKRKANGGFIMSASHNPGGPEYDWG 192
            A Q I+++AA NGV + +VG+ GILSTPA S VIRKR A GG I+SASHNPGGP+ D+G
Sbjct: 65  TAVQTILRMAAANGVARAVVGRGGILSTPAASCVIRKRGAIGGVILSASHNPGGPDGDFG 124

Query: 193 IKFNYSSGQPAPETITDKIYGNTLSISEIKVAEIPDIDLSQVGVTKYGNFSVEVIDPVSD 252
           IKFN ++G PAPE++TD  +  + +I+E K  E PD+DL ++G T  G  +VEVIDPV+D
Sbjct: 125 IKFNAANGGPAPESMTDAFFARSKAITEYKTLESPDLDLDRLGETALGGIAVEVIDPVAD 184

Query: 253 YLELMEDVFDFDLIRGLLSRSDFGFMFDAMHAVTGAYAKPIFVDNLGAKPDSISNGVPLE 312
           Y ELME +FD   IR L + S F  +FDAMHAVTG YA  I    LGA   ++ NG PLE
Sbjct: 185 YAELMESLFDMAAIRKLFA-SGFRMVFDAMHAVTGPYATEILERRLGAPAGTVINGTPLE 243

Query: 313 DFGHGHPDPNLTYAKDLVDVMYRDNGPDFGAASDGDGDRNMVLGNKFFVTPSDSVAIIAA 372
           DFG  HPDPNL +A++LV  ++  + PDFGAASDGDGDRNM+LG   FV+PSDS+A++AA
Sbjct: 244 DFGGHHPDPNLAHAEELVGRLFGPDAPDFGAASDGDGDRNMILGRNVFVSPSDSLAVLAA 303

Query: 373 NAQEAIPYFRAGPKGLARSMPTSGALDRVAEKLKLPFFEVPTGWKFFGNLMDAGKLSICG 432
           NA   +P F+ G  G+ARSMPTS A+DRVA KL +  +E PTGWKFFG L+DAG++++CG
Sbjct: 304 NATH-VPAFKGGLAGVARSMPTSRAVDRVAAKLGISCYETPTGWKFFGTLLDAGRINLCG 362

Query: 433 EESFGTGSDHIREKDGIWAVLAWLSILAHRNKDTKPGDKLVSVADVVKEYWATYGRNFFS 492
           EESFGTG+DH+REKDG+WAVL WL++LA R          +SVA+++ E+W TYGR ++ 
Sbjct: 363 EESFGTGADHVREKDGLWAVLMWLNVLAARG---------LSVAELMAEHWGTYGRTYYG 413

Query: 493 RYDYEECESEGANKMIEYLREILSKSKAGDVYGNYVLQFADDFSYTDPVDGSVASKQGVR 552
           R+DYE    E A+ +I  LR  LS S AG   G   +  AD+F+YTDPVDGS + +QG+R
Sbjct: 414 RHDYEAIPQEAADALIAELRGTLS-SLAGTDLGGRTVAAADEFAYTDPVDGSRSERQGLR 472

Query: 553 FVFTDGSRIIFRLSGTGSAGATVRIYIEQFEPDVSKHDVDAQIALKPLIDLALSVSKLKD 612
             F DGSRI++RLSGTG++GAT+R+Y E++EP   +H +DA +ALKPL DLA  ++ ++ 
Sbjct: 473 VGFEDGSRIVYRLSGTGTSGATLRVYFERYEPVGGEHGLDAPVALKPLADLAAELAGIER 532

Query: 613 FTGREKPTVIT 623
            TGR KP V T
Sbjct: 533 HTGRTKPDVAT 543


Lambda     K      H
   0.317    0.136    0.399 

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: 1013
Number of extensions: 48
Number of successful extensions: 6
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: 623
Length of database: 543
Length adjustment: 36
Effective length of query: 587
Effective length of database: 507
Effective search space:   297609
Effective search space used:   297609
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: 53 (25.0 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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