Alignments for a candidate for pgmA in Bacteroides clarus YIT 12056

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Bacteroides clarus YIT 12056

Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate WP_009121716.1 BUB52_RS05025 phospho-sugar mutase

Query= SwissProt::P18159
         (581 letters)



>NCBI__GCF_900129655.1:WP_009121716.1
          Length = 580

 Score =  458 bits (1179), Expect = e-133
 Identities = 244/549 (44%), Positives = 359/549 (65%), Gaps = 16/549 (2%)

Query: 8   ERWKQTEHLDLELK---ERLIELEGDEQALEDCFYKDLEFGTGGMRGEIGAGTNRMNIYT 64
           E+W  T   D E +   +R++E   D+  L +CFYKDLEFGTGG+RG +GAG+NRMNIYT
Sbjct: 15  EKWL-TPAYDAETQAEVKRMLE-NPDKTELIECFYKDLEFGTGGLRGIMGAGSNRMNIYT 72

Query: 65  VRKASAGFAAYISKQGEEAKKRGVVIAYDSRHKSPEFAMEAAKTLATQGIQTYVFDELRP 124
           V  A+ G A Y++K  ++ ++  VV+ +D R+ S +FA  +A   +  GI+ Y+FD+LRP
Sbjct: 73  VGAATQGLANYLNKCFKDKEQISVVVGHDCRNNSRKFAEISADIFSANGIKVYLFDDLRP 132

Query: 125 TPELSFAVRQLNAYGGIVVTASHNPPEYNGYKVYGDDGGQLPPKEADIVIEQVNAIENEL 184
           TPE+SFA+R L    GI +TASHNP EYNGYK Y DDG Q+       +I++VN      
Sbjct: 133 TPEVSFAIRHLGCQSGINLTASHNPKEYNGYKAYWDDGAQVLAPHDTAIIDEVN------ 186

Query: 185 TITVDEENKLKEKGLIKIIGEDIDKVYTEKLTSISVHPE-LSEEVDVKVVFTPLHGTANK 243
            +TV++      K LI+IIGEDIDKVY +K+ ++S+ PE +  + D+ +V+TPLHG    
Sbjct: 187 KVTVEDIKFQGNKDLIQIIGEDIDKVYLDKVHTLSIDPEVIKRQKDLSIVYTPLHGAGRV 246

Query: 244 PVRRGLEALGYKNVTVVKEQELPDSNFSTVTSPNPEEHAAFEYAIKLGEEQNADILIATD 303
            +   L+  G++NV  V EQ +   +F TV SPNPE   A   AI+L ++ +ADI++A+D
Sbjct: 247 LIPASLKEWGFENVHCVPEQMVKSGDFPTVISPNPENAEALSMAIELAKKIDADIVMASD 306

Query: 304 PDADRLGIAVKNDQGKYTVLTGNQTGALLLHYLLSEKKKQGILPDNGVVLKTIVTSEIGR 363
           PDADR+G+A K+D+G++ ++ GNQT  L L+Y++  +   G +     ++KTIVT+E+ +
Sbjct: 307 PDADRVGMACKDDKGEWVLINGNQTCLLFLYYIIKNRIATGKMQPTDFIVKTIVTTELIK 366

Query: 364 AVASSFGLDTIDTLTGFKFIGEKIKEYEASGQYTFQFGYEESYGYLIGDFARDKDAIQAA 423
           AVA    ++ +D  TGFK+I  +I+  E   QY    G EESYG+L  DF RDKDA+ A 
Sbjct: 367 AVADKNKIEMLDCYTGFKWIAREIRLREGKQQYI--GGGEESYGFLAEDFVRDKDAVSAC 424

Query: 424 LLAVEVCAFYKKQGMSLYEALINLFNEYGFYREGLKSLTLKGKQGAEQIEAILASFRQNP 483
            L  E+CA+ K QG +LY+ L++++ EYGF +E   ++   GK GA++I+A++ +FR NP
Sbjct: 425 SLLAEICAWAKDQGKTLYDILMDIYVEYGFSKETTVNVVKPGKSGADEIKAMMDNFRANP 484

Query: 484 PQKMAGKQVVTAEDYAVSKRTLLTESKEEAIDLPK-SNVLKYFLEDGSWFCLRPSGTEPK 542
           P+++ G  V   +DY   K T   +     +D+P+ SNVL+YF EDG+   +RPSGTEPK
Sbjct: 485 PKEIGGSAVSLIKDYKTLKAT-DAKGNVTDLDMPETSNVLQYFTEDGTKISVRPSGTEPK 543

Query: 543 VKFYFAVKG 551
           +KFY  VKG
Sbjct: 544 IKFYIEVKG 552


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: 802
Number of extensions: 26
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: 581
Length of database: 580
Length adjustment: 36
Effective length of query: 545
Effective length of database: 544
Effective search space:   296480
Effective search space used:   296480
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 2024 update 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