GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pgmA in Synechococcus elongatus PCC 7942

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate Synpcc7942_0156 Synpcc7942_0156 phosphoglucomutase

Query= BRENDA::Q9SCY0
         (623 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_0156 Synpcc7942_0156
           phosphoglucomutase
          Length = 543

 Score =  629 bits (1621), Expect = 0.0
 Identities = 315/557 (56%), Positives = 412/557 (73%), Gaps = 14/557 (2%)

Query: 67  IEIKSLPTKPIEGQKTGTSGLRKKVKVFMEDNYLANWIQALFNSLPLEDYKNATLVLGGD 126
           + I ++ T+    QK GTSGLRK+V VF + +YL N++Q++F+SL  E Y+  TLVLGGD
Sbjct: 1   MNIHTVATQAFSDQKPGTSGLRKQVPVFQKRHYLENFVQSIFDSL--EGYQGQTLVLGGD 58

Query: 127 GRYFNKEASQIIIKIAAGNGVGQILVGKEGILSTPAVSAVIRKRKANGGFIMSASHNPGG 186
           GRY+N+ A Q I+K+AA NG G++LVG+ GILSTPAVS +IR+  A GG I+SASHNPGG
Sbjct: 59  GRYYNRTAIQTILKMAAANGWGRVLVGQGGILSTPAVSNLIRQNGAFGGIILSASHNPGG 118

Query: 187 PEYDWGIKFNYSSGQPAPETITDKIYGNTLSISEIKVAEIPDIDLSQVGVTKYGNFSVEV 246
           PE D+GIK+N S+G PAPE +TD IY  +L I   ++ E  D+DL ++G  + G  +VEV
Sbjct: 119 PEGDFGIKYNISNGGPAPEKVTDAIYACSLKIEAYRILEAGDVDLDRLGSQQLGEMTVEV 178

Query: 247 IDPVSDYLELMEDVFDFDLIRGLLSRSDFGFMFDAMHAVTGAYAKPIFVDNLGAKPDSIS 306
           ID V+DY  LM+ +FDFD IR  L R       D+MHAVTG YA  IF   LGA   ++ 
Sbjct: 179 IDSVADYSRLMQSLFDFDRIRDRL-RGGLRIAIDSMHAVTGPYATTIFEKELGAAAGTVF 237

Query: 307 NGVPLEDFGHGHPDPNLTYAKDLVDVMYRDNGPDFGAASDGDGDRNMVLGNKFFVTPSDS 366
           NG PLEDFG GHPDPNL YA DLV++++ D  PDFGAASDGDGDRNM+LGN FFVTPSDS
Sbjct: 238 NGKPLEDFGGGHPDPNLVYAHDLVELLFGDRAPDFGAASDGDGDRNMILGNHFFVTPSDS 297

Query: 367 VAIIAANAQEAIPYFRAGPKGLARSMPTSGALDRVAEKLKLPFFEVPTGWKFFGNLMDAG 426
           +AI+AANA   +P +R G  G+ARSMPTS A DRVA+ L LP +E PTGWKFFGNL+DA 
Sbjct: 298 LAILAANA-SLVPAYRNGLSGIARSMPTSAAADRVAQALNLPCYETPTGWKFFGNLLDAD 356

Query: 427 KLSICGEESFGTGSDHIREKDGIWAVLAWLSILAHRNKDTKPGDKLVSVADVVKEYWATY 486
           ++++CGEESFGTGS+H+REKDG+WAVL WL+ILA R +         SVA++V+E+W TY
Sbjct: 357 RVTLCGEESFGTGSNHVREKDGLWAVLFWLNILAVREQ---------SVAEIVQEHWRTY 407

Query: 487 GRNFFSRYDYEECESEGANKMIEYLREILSKSKAGDVYGNYVLQFADDFSYTDPVDGSVA 546
           GRN++SR+DYE  ES+ A+ +++ LR  L  S  G   G Y + +ADDF Y DPVDGS++
Sbjct: 408 GRNYYSRHDYEGVESDRASTLVDKLRSQL-PSLTGQKLGAYTVAYADDFRYEDPVDGSIS 466

Query: 547 SKQGVRFVFTDGSRIIFRLSGTGSAGATVRIYIEQFEPDVSKHDVDAQIALKPLIDLALS 606
            +QG+R  F DGSR++FRLSGTG+AGAT+R+Y+E+FE D +K  +D Q+AL  LI +A  
Sbjct: 467 EQQGIRIGFEDGSRMVFRLSGTGTAGATLRLYLERFEGDTTKQGLDPQVALADLIAIADE 526

Query: 607 VSKLKDFTGREKPTVIT 623
           V+++   TG ++PTVIT
Sbjct: 527 VAQITTLTGFDQPTVIT 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: 1002
Number of extensions: 41
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