Alignments for a candidate for pgmA in Desulfobulbus mediterraneus DSM 13871

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Desulfobulbus mediterraneus DSM 13871

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_028585974.1 G494_RS0120225 phosphomannomutase/phosphoglucomutase

Query= BRENDA::Q8PGN7
         (450 letters)



>NCBI__GCF_000429965.1:WP_028585974.1
          Length = 457

 Score =  536 bits (1382), Expect = e-157
 Identities = 266/459 (57%), Positives = 334/459 (72%), Gaps = 11/459 (2%)

Query: 1   MPMTLPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALS 60
           M  ++  F AYDIRG+VPD+L+E+LA  IG+A         +VLGHD+RL SPA+  AL+
Sbjct: 1   MSDSVRCFTAYDIRGKVPDDLDEELAALIGLAFIEHFAAKKIVLGHDMRLTSPAISRALT 60

Query: 61  AGLRASGRDVIDIGLCGTEEVY---FQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARP 117
             + A G DV+DIGLCGTEEVY   F        GG+M+TASHNP  YNGMKLV+ +ARP
Sbjct: 61  RAVLARGCDVVDIGLCGTEEVYHRVFAGADQGVDGGIMITASHNPAAYNGMKLVQREARP 120

Query: 118 ISSDTGLFAIRDTVAADT------AAPGEPTASEQSRTDKTAYLEHLLSYVDRSTLKPLK 171
           +S ++GL  I   V+  T         G P  S +   +K  Y++HLLS VD   LKPLK
Sbjct: 121 VSGESGLAEIEARVSDTTWRRQAGKDSGVPPGSYRLEEEKGGYIQHLLSSVDLEQLKPLK 180

Query: 172 LVVNAGNGGAGLIVDLLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNG 231
           LVVN GNG AG I+DLL  HLPF F+R+  +PDG+FPNG+PNPLLPE R  TA+AV+++G
Sbjct: 181 LVVNPGNGCAGPIIDLLESHLPFTFIRLQEQPDGSFPNGVPNPLLPEKRAVTAEAVREHG 240

Query: 232 ADFGIAWDGDFDRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQV 291
           AD GIAWDGDFDRCFF+D TGRFIEGYY+VGLL  AIL + PG  ++HDPRLTWNT+E V
Sbjct: 241 ADLGIAWDGDFDRCFFYDETGRFIEGYYIVGLLGTAILQQHPGATILHDPRLTWNTIEMV 300

Query: 292 EEAGGIPVLCKSGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQ 351
           E AGG P++ ++GHAFIKE MR+ + VYGGEMSAHHYFR+F Y DSGM+PWLL+ +L+S 
Sbjct: 301 EAAGGHPLMTRTGHAFIKENMRAADGVYGGEMSAHHYFRDFGYCDSGMVPWLLVTQLMSS 360

Query: 352 SGRSLADLVEARMQKFPCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQW 411
           SG+ L+ +V+ RMQ+FP SGEIN  VAD    + +V E Y     ELD+TDGIS  + ++
Sbjct: 361 SGQPLSAMVDDRMQRFPVSGEINSTVADPDGIIRQVEERYR--DGELDHTDGISVSYPEY 418

Query: 412 RFNLRSSNTEPLLRLNVETRGDAALLETRTQEISNLLRG 450
           RFN+R SNTEP+LRLNVETRGDAALL   T+E+  L+RG
Sbjct: 419 RFNIRKSNTEPVLRLNVETRGDAALLHRTTEELLALIRG 457


Lambda     K      H
   0.319    0.136    0.404 

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: 676
Number of extensions: 32
Number of successful extensions: 4
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: 450
Length of database: 457
Length adjustment: 33
Effective length of query: 417
Effective length of database: 424
Effective search space:   176808
Effective search space used:   176808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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