Alignments for a candidate for pgmA in Sulfuritalea hydrogenivorans DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Sulfuritalea hydrogenivorans DSM 22779

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_041099655.1 SUTH_RS12465 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= BRENDA::Q9SCY0
         (623 letters)



>NCBI__GCF_000828635.1:WP_041099655.1
          Length = 547

 Score =  620 bits (1600), Expect = 0.0
 Identities = 322/561 (57%), Positives = 407/561 (72%), Gaps = 18/561 (3%)

Query: 67  IEIKSLPTKPIEGQKTGTSGLRKKVKVFMEDNYLANWIQALFNSLPLEDYKNATLVLGGD 126
           + I ++ T P   QK GTSGLRKKV VF    YL N++QA+F+++       +TLVLGGD
Sbjct: 1   MNIATVITTPFSDQKPGTSGLRKKVTVFRTPGYLENFVQAVFDTIDAPP--GSTLVLGGD 58

Query: 127 GRYFNKEASQIIIKIAAGNGVGQILVGKEGILSTPAVSAVIRKRKANGGFIMSASHNPGG 186
           GRY N+EA Q+I+++AA  G+ ++LVG+ GILSTPA S VIRK    GG I+SASHNPGG
Sbjct: 59  GRYHNREAIQVILRMAAAAGIAKVLVGRGGILSTPAASRVIRKYGCFGGLILSASHNPGG 118

Query: 187 PEYDWGIKFNYSSGQPAPETITDKIYGNTLSISEIKVAEIPDIDLSQVGVTKYGNFSVEV 246
           PE D+GIK+N  +G PAPE ITD I+  +  ++  ++A+ PD+DL + G    G+  VE+
Sbjct: 119 PEGDFGIKYNTGNGGPAPEKITDAIFARSRELTRYRIADAPDLDLDRPGRHGLGDMVVEI 178

Query: 247 IDPVSDYLELMEDVFDFDLIRGLLSRSDFGFMFDAMHAVTGAYAKPIFVDNLGAKPDSIS 306
           IDPV+DY ELME +FDF  IR L+  S F   FDAMHAVTG YA+ I    LGA   ++ 
Sbjct: 179 IDPVADYAELMESLFDFAAIRTLIG-SGFRLCFDAMHAVTGPYAREIIEARLGAPAGTVI 237

Query: 307 NGVPLEDFGHGHPDPNLTYAKDLVDVMY----RDNGPDFGAASDGDGDRNMVLGNKFFVT 362
           NGVPLEDFG GHPDPNLTYA  LV +MY     +  PDFGAASDGDGDRNM+LG  FFVT
Sbjct: 238 NGVPLEDFGGGHPDPNLTYADQLVAIMYGGDDANPAPDFGAASDGDGDRNMILGRHFFVT 297

Query: 363 PSDSVAIIAANAQEAIPYFRAGPKGLARSMPTSGALDRVAEKLKLPFFEVPTGWKFFGNL 422
           PSDS+AIIAANA  A P +  G  G+ARSMPTS A DRVAEKL +P +E PTGWKFFGNL
Sbjct: 298 PSDSLAIIAANAALA-PGYADGIAGIARSMPTSAAADRVAEKLGVPCYETPTGWKFFGNL 356

Query: 423 MDAGKLSICGEESFGTGSDHIREKDGIWAVLAWLSILAHRNKDTKPGDKLVSVADVVKEY 482
           MDAGK+++CGEESFGTGS H+REKDG+WAVL WL+ILA+           +SVA++V  +
Sbjct: 357 MDAGKVTLCGEESFGTGSSHVREKDGLWAVLFWLNILANSR---------LSVAEIVHRH 407

Query: 483 WATYGRNFFSRYDYEECESEGANKMIEYLREILSKSKAGDVYGNYVLQFADDFSYTDPVD 542
           WA YGRN +SR+DYE   S+ A  ++  +R   +    G  +G+Y ++F DDFSYTDP+D
Sbjct: 408 WAGYGRNVYSRHDYEALPSDVAAGVMAQVRGRFA-DLPGQRFGDYRVKFCDDFSYTDPID 466

Query: 543 GSVASKQGVRFVFTDGSRIIFRLSGTGSAGATVRIYIEQFEPDVSKHDVDAQIALKPLID 602
           GS+++ QG+R  F DGSRI+FRLSGTG+ GAT+RIY+E FEPD ++  VDAQ AL PLI 
Sbjct: 467 GSLSTGQGLRIGFEDGSRIVFRLSGTGTEGATLRIYLEAFEPDPARQRVDAQQALAPLIA 526

Query: 603 LALSVSKLKDFTGREKPTVIT 623
           +A  +S+LK  TGRE+PTVIT
Sbjct: 527 IADQLSELKQRTGRERPTVIT 547


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: 1079
Number of extensions: 59
Number of successful extensions: 7
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: 547
Length adjustment: 36
Effective length of query: 587
Effective length of database: 511
Effective search space:   299957
Effective search space used:   299957
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 Apr 09 2024. 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:

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