Alignments for a candidate for pgmA in Methylohalobius crimeensis 10Ki

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Methylohalobius crimeensis 10Ki

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_022949404.1 H035_RS0112995 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= BRENDA::Q9SCY0
         (623 letters)



>NCBI__GCF_000421465.1:WP_022949404.1
          Length = 545

 Score =  596 bits (1536), Expect = e-174
 Identities = 301/558 (53%), Positives = 403/558 (72%), Gaps = 14/558 (2%)

Query: 67  IEIKSLPTKPIEGQKTGTSGLRKKVKVFMED-NYLANWIQALFNSLPLEDYKNATLVLGG 125
           ++I++ PT P   QK GTSGLRKK +VF+E  +YL N++Q++F+ LP  D K  TLVLGG
Sbjct: 1   MQIETRPTTPFPDQKPGTSGLRKKTRVFLETPHYLENFVQSIFDCLP--DRKGKTLVLGG 58

Query: 126 DGRYFNKEASQIIIKIAAGNGVGQILVGKEGILSTPAVSAVIRKRKANGGFIMSASHNPG 185
           DGRYFN+ A Q IIKIA  N  G +LV ++G+LSTPA S +IRK +A GG ++SASHNPG
Sbjct: 59  DGRYFNRPALQTIIKIAVANEFGTLLVAQKGLLSTPAASHLIRKNRALGGIVLSASHNPG 118

Query: 186 GPEYDWGIKFNYSSGQPAPETITDKIYGNTLSISEIKVAEIPDIDLSQVGVTKYGNFSVE 245
           G + D+GIK+N  +G PAPE+ T+ IY  +  I E ++A+IPDIDL ++   ++GN ++ 
Sbjct: 119 GRDGDFGIKYNIDNGGPAPESYTNAIYQRSREIGEYRIAQIPDIDLDRLDEHRFGNTTIR 178

Query: 246 VIDPVSDYLELMEDVFDFDLIRGLLSRSDFGFMFDAMHAVTGAYAKPIFVDNLGAKPDSI 305
           VIDPV+DY+ELM  +FDFD +R  L+       FDAMHAVTG YAK I  + LGA P S+
Sbjct: 179 VIDPVADYVELMTQLFDFDRMRNALTTGVASVCFDAMHAVTGPYAKRILEEELGAGPGSV 238

Query: 306 SNGVPLEDFGHGHPDPNLTYAKDLVDVMYRDNGPDFGAASDGDGDRNMVLGNKFFVTPSD 365
            N  P EDFG GHPDPNL YA+ LV  MY  + P  GAASDGDGDRNM+LG KFFVTPSD
Sbjct: 239 INAEPKEDFGGGHPDPNLAYAEALVKKMYGPDAPTLGAASDGDGDRNMILGQKFFVTPSD 298

Query: 366 SVAIIAANAQEAIPYFRAGPKGLARSMPTSGALDRVAEKLKLPFFEVPTGWKFFGNLMDA 425
           S+A++AANA   IP +R G +G+ARSMPTS A+D+VAE   +P +E PTGWKFFGNL+DA
Sbjct: 299 SLAVLAANAHR-IPGYRNGLRGVARSMPTSRAVDQVAEAFGIPCYETPTGWKFFGNLLDA 357

Query: 426 GKLSICGEESFGTGSDHIREKDGIWAVLAWLSILAHRNKDTKPGDKLVSVADVVKEYWAT 485
           GK+++CGEESFGTGSDH+REKDG+WAVL WL+I+    +          VA +V+++W  
Sbjct: 358 GKITLCGEESFGTGSDHVREKDGLWAVLFWLNIIVASEQ---------PVATLVRDHWRR 408

Query: 486 YGRNFFSRYDYEECESEGANKMIEYLREILSKSKAGDVYGNYVLQFADDFSYTDPVDGSV 545
           +GR+++SR+DYE  +S  A  ++ +LR  L  S  G   G Y ++ ADDFSY+DPVD SV
Sbjct: 409 FGRHYYSRHDYEALDSTVAQGIMNHLRGQLD-SLVGRKLGIYTVRQADDFSYSDPVDHSV 467

Query: 546 ASKQGVRFVFTDGSRIIFRLSGTGSAGATVRIYIEQFEPDVSKHDVDAQIALKPLIDLAL 605
            + QG+R +    +R+++RLSGTG+ GAT+R+YIE+FE D ++ D D Q  L  LI+LA 
Sbjct: 468 TTGQGLRILLEPEARLVYRLSGTGTEGATLRVYIERFESDPTRQDSDPQEGLADLIELAE 527

Query: 606 SVSKLKDFTGREKPTVIT 623
            +S++K  +GR +P+VIT
Sbjct: 528 DLSEVKARSGRSEPSVIT 545


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: 974
Number of extensions: 57
Number of successful extensions: 5
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: 545
Length adjustment: 36
Effective length of query: 587
Effective length of database: 509
Effective search space:   298783
Effective search space used:   298783
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 24 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:

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