GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS02670
          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:

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