Alignments for a candidate for pgmA in Synechococcus elongatus PCC 7942

GapMind for catabolism of small carbon sources

Alignments 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)



>FitnessBrowser__SynE:Synpcc7942_0156
          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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources