GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Bacteroides faecis MAJ27

Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate WP_010538804.1 KCY_RS0120345 phospho-sugar mutase

Query= SwissProt::P18159
         (581 letters)



>NCBI__GCF_000226135.1:WP_010538804.1
          Length = 581

 Score =  466 bits (1199), Expect = e-135
 Identities = 248/550 (45%), Positives = 364/550 (66%), Gaps = 17/550 (3%)

Query: 8   ERWKQTEHLDLELK---ERLIELEGDEQALEDCFYKDLEFGTGGMRGEIGAGTNRMNIYT 64
           E+W  T   D E +   +R++E E D+  L + FYKDLEFGTGG+RG +G G+NRMNIYT
Sbjct: 15  EKWL-TPAYDAETQAEVKRMLENE-DKTELIEAFYKDLEFGTGGLRGIMGVGSNRMNIYT 72

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

Query: 125 TPELSFAVRQLNAYGGIVVTASHNPPEYNGYKVYGDDGGQ-LPPKEADIVIEQVNAIENE 183
           TPE+SFA+R L    GI++TASHNP EYNGYK Y DDG Q L P +A I I++VN I + 
Sbjct: 133 TPEMSFAIRHLGCQSGIILTASHNPKEYNGYKAYWDDGAQVLAPHDAGI-IDEVNNIASA 191

Query: 184 LTITVDEENKLKEKGLIKIIGEDIDKVYTEKLTSISVHPE-LSEEVDVKVVFTPLHGTAN 242
             I            LI+IIGEDIDK+Y + + ++S+ PE ++   D+K+V+TP+HGT  
Sbjct: 192 ADIKFQ-----GNPDLIQIIGEDIDKIYLDMVKTVSIDPEAIARHKDMKIVYTPIHGTGM 246

Query: 243 KPVRRGLEALGYKNVTVVKEQELPDSNFSTVTSPNPEEHAAFEYAIKLGEEQNADILIAT 302
             + R L+  G++NV  V EQ + D NF TV SPNPE   A   A+ L +E +A++++A+
Sbjct: 247 MLIPRALKMWGFENVFTVPEQMIKDGNFPTVVSPNPENAEALSMAVNLAKEIDAELVMAS 306

Query: 303 DPDADRLGIAVKNDQGKYTVLTGNQTGALLLHYLLSEKKKQGILPDNGVVLKTIVTSEIG 362
           DPDADR+GIA K+D+G++ ++ GNQT  + L+Y+L++ K+ G +  N   +KTIVT+E+ 
Sbjct: 307 DPDADRVGIACKDDKGEWVLINGNQTCMMYLYYILTQYKQLGKIQGNEFCVKTIVTTELI 366

Query: 363 RAVASSFGLDTIDTLTGFKFIGEKIKEYEASGQYTFQFGYEESYGYLIGDFARDKDAIQA 422
           + +A    ++ +D  TGFK+I  +I+  E   +Y    G EESYG+L  DF RDKDA+ A
Sbjct: 367 KKIADKNNIEMLDCYTGFKWIAREIRLREGKKKYI--GGGEESYGFLAEDFVRDKDAVSA 424

Query: 423 ALLAVEVCAFYKKQGMSLYEALINLFNEYGFYREGLKSLTLKGKQGAEQIEAILASFRQN 482
             L  EV A+ K  G SLY+ L++++ EYGF +E   ++   GK GAE+I+A++ +FR N
Sbjct: 425 CCLIAEVAAWAKDNGKSLYQLLLDIYVEYGFSKEFTVNVVKPGKSGAEEIKAMMENFRAN 484

Query: 483 PPQKMAGKQVVTAEDYAVSKRTLLTESKEEAIDLPK-SNVLKYFLEDGSWFCLRPSGTEP 541
           PP+++ G +V+ ++DY   K+T   E K  A+D+P+ SNVL+YF EDGS   +RPSGTEP
Sbjct: 485 PPKELGGSKVILSKDYKTLKQT-DAEGKVTALDMPETSNVLQYFTEDGSKVSVRPSGTEP 543

Query: 542 KVKFYFAVKG 551
           K+KFY  V+G
Sbjct: 544 KIKFYMEVQG 553


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: 822
Number of extensions: 33
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: 581
Length adjustment: 36
Effective length of query: 545
Effective length of database: 545
Effective search space:   297025
Effective search space used:   297025
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:

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:

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:

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:

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