Alignments for a candidate for pgmA in Thermoactinomyces daqus H-18

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Thermoactinomyces daqus H-18

Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate WP_033102081.1 JG50_RS0115725 phospho-sugar mutase

Query= SwissProt::P18159
         (581 letters)



>NCBI__GCF_000763315.1:WP_033102081.1
          Length = 565

 Score =  630 bits (1624), Expect = 0.0
 Identities = 315/572 (55%), Positives = 416/572 (72%), Gaps = 13/572 (2%)

Query: 1   MTWRKSYERWKQTEHLDLELKERLIELEGDEQALEDCFYKDLEFGTGGMRGEIGAGTNRM 60
           M +R++ +RW + + LD +L+  L E+  DE+ LED FY  L FGT GMRG IGAGTNRM
Sbjct: 1   MDYRQAVDRWLKFQDLDRDLRRELEEIT-DEKELEDRFYTSLTFGTAGMRGIIGAGTNRM 59

Query: 61  NIYTVRKASAGFAAYISKQGEEAKKRGVVIAYDSRHKSPEFAMEAAKTLATQGIQTYVFD 120
           N YTVRKA+ G A +I  QGEEAKK+GVVIAYD RH+SPEFA EA   LA  GI+ YVF 
Sbjct: 60  NRYTVRKATQGLARFILNQGEEAKKKGVVIAYDCRHQSPEFAREAGLVLAQNGIKAYVFA 119

Query: 121 ELRPTPELSFAVRQLNAYGGIVVTASHNPPEYNGYKVYGDDGGQLPPKEADIVIEQVNAI 180
           ELRPTPELSFAVR L    GI++TASHNPPEYNGYKVYG DG Q+    A+ V+E++  +
Sbjct: 120 ELRPTPELSFAVRHLGTAAGIMITASHNPPEYNGYKVYGSDGAQIATDLANAVLEEIGRV 179

Query: 181 ENELTITVDEENKLKEKGLIKIIGEDIDKVYTEKLTSISVHPELSEEVDVKVVFTPLHGT 240
            +ELT+ +    + +  GL ++IGE+ID  Y E+L S+++ P +    D+K+V+TPLHGT
Sbjct: 180 PDELTVPIMPLEEARAAGLFEVIGEEIDDAYQERLRSLAMQP-VQNNRDLKIVYTPLHGT 238

Query: 241 ANKPVRRGLEALGYKNVTVVKEQELPDSNFSTVTSPNPEEHAAFEYAIKLGEEQNADILI 300
            NKPVRR L  LG+  V VV++QE PD +FSTV SPNPEEH AF  AI++ E   ADI++
Sbjct: 239 GNKPVRRILRDLGFGQVQVVEQQEKPDPDFSTVRSPNPEEHEAFAQAIEIAERTGADIIM 298

Query: 301 ATDPDADRLGIAVKNDQGKYTVLTGNQTGALLLHYLLSEKKKQGILPDNGVVLKTIVTSE 360
            TDPDADR+G+  +++ G+++VLTGNQ GALLL YLL+ +K++G LP+NGV++KTIVTSE
Sbjct: 299 GTDPDADRVGVVARDETGEFSVLTGNQLGALLLDYLLARRKERGNLPENGVMIKTIVTSE 358

Query: 361 IGRAVASSFGLDTIDTLTGFKFIGEKIKEYEASGQYTFQFGYEESYGYLIGDFARDKDAI 420
           +G  +A+ +G++TI+TLTGFKFI ++IK+Y  SG+ TF FGYEESYGYLIGDF RDKDA+
Sbjct: 359 LGAKIAARYGVETINTLTGFKFIADRIKQYAESGEKTFLFGYEESYGYLIGDFCRDKDAV 418

Query: 421 QAALLAVEVCAFYKKQGMSLYEALINLFNEYGFYREGLKSLTLKGKQGAEQIEAILASFR 480
           QA ++A E+ A+YK+QG++LY+AL  LF+ YG ++E L SLTLKG  G +++ AI+   R
Sbjct: 419 QACMVAAEMAAYYKRQGLTLYQALRRLFDRYGTHQEELVSLTLKGVDGIKRMRAIMERLR 478

Query: 481 QNPPQKMAGKQVVTAEDYAVSKRTLLTESKEEAIDLPKSNVLKYFLEDGSWFCLRPSGTE 540
           + P ++  G  V   +DY+                LPK++VLKY  EDGSWF +RPSGTE
Sbjct: 479 RFPLREAGGITVREQKDYS-----------RGIEGLPKADVLKYLFEDGSWFAIRPSGTE 527

Query: 541 PKVKFYFAVKGSSLEDSEKRLAVLSEDVMKTV 572
           PK+KFYFA  G + E++  RL  L  DVMK V
Sbjct: 528 PKIKFYFASVGENGEEARTRLENLKRDVMKIV 559


Lambda     K      H
   0.313    0.133    0.371 

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: 903
Number of extensions: 34
Number of successful extensions: 3
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: 581
Length of database: 565
Length adjustment: 36
Effective length of query: 545
Effective length of database: 529
Effective search space:   288305
Effective search space used:   288305
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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