GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Paludibacter propionicigenes WB4

Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate WP_013444375.1 PALPR_RS04220 phospho-sugar mutase

Query= SwissProt::P18159
         (581 letters)



>NCBI__GCF_000183135.1:WP_013444375.1
          Length = 582

 Score =  459 bits (1182), Expect = e-133
 Identities = 243/532 (45%), Positives = 346/532 (65%), Gaps = 10/532 (1%)

Query: 23  RLIELEGDEQALEDCFYKDLEFGTGGMRGEIGAGTNRMNIYTVRKASAGFAAYISKQGEE 82
           RL+E E D+  L + FY+DLEFGTGG+RG +G GTNRMNIYTV  A+ G + Y+  Q  +
Sbjct: 32  RLLEAE-DKSELIESFYRDLEFGTGGLRGIMGVGTNRMNIYTVGAATQGLSNYLKAQFPD 90

Query: 83  AKKRGVVIAYDSRHKSPEFAMEAAKTLATQGIQTYVFDELRPTPELSFAVRQLNAYGGIV 142
             +  VVI +D R+ S  F+  +A   +  GI+ Y+F++LRPTPE SFA+R L    GI+
Sbjct: 91  VPQLSVVIGHDCRNNSRLFSEISANIFSANGIKVYLFEDLRPTPEASFAIRHLGCQSGII 150

Query: 143 VTASHNPPEYNGYKVYGDDGGQLPPKEADIVIEQVNAIENELTITVDEENKLKEKGLIKI 202
           +TASHNP EYNGYK Y +DG Q+     + VI +VN I +     VD+        LI+I
Sbjct: 151 LTASHNPKEYNGYKAYWNDGAQMVAPHDENVITEVNKIAS-----VDDIKFEGNPALIEI 205

Query: 203 IGEDIDKVYTEKLTSISVHPE-LSEEVDVKVVFTPLHGTANKPVRRGLEALGYKNVTVVK 261
           IGE+IDK++ E +  +S+ PE +    ++K+V+TP+HGT  K + R L+  G+ N+  V 
Sbjct: 206 IGEEIDKLFIENIKKLSLSPESIKRNSNLKIVYTPIHGTGVKLIPRALKEYGFTNIIAVP 265

Query: 262 EQELPDSNFSTVTSPNPEEHAAFEYAIKLGEEQNADILIATDPDADRLGIAVKNDQGKYT 321
           EQ +   NF TV SPNPEE AA + A+K   E +ADI++A+DPDADRLGIAVKND+G++ 
Sbjct: 266 EQNVVSGNFPTVVSPNPEEPAALDMAVKKAIETDADIVMASDPDADRLGIAVKNDKGEWI 325

Query: 322 VLTGNQTGALLLHYLLSEKKKQGILPDNGVVLKTIVTSEIGRAVASSFGLDTIDTLTGFK 381
           ++ GNQT  L ++YL+   K+ G L  N  ++KTIVT+EI + +A   G++  D  TGFK
Sbjct: 326 LVNGNQTALLFIYYLIRRWKELGKLNGNQYIVKTIVTTEIIKQIAERNGVEMFDCFTGFK 385

Query: 382 FIGEKIKEYEASGQYTFQFGYEESYGYLIGDFARDKDAIQAALLAVEVCAFYKKQGMSLY 441
           +I   I+E E   +Y    G EESYG+L  +FARDKDA+ +  +  E+ A+ K  G +L+
Sbjct: 386 WIAAVIRENEGKKEYI--GGGEESYGFLPEEFARDKDAVSSCTVMAEIAAWAKDNGKTLF 443

Query: 442 EALINLFNEYGFYREGLKSLTLKGKQGAEQIEAILASFRQNPPQKMAGKQVVTAEDYAVS 501
           E L +++ EYG+ +E   S+  KGK GAE+I  ++  FR NPP+++AG +V   +DY   
Sbjct: 444 ELLQDIYVEYGYGKEKGISVVRKGKSGAEEIAQMMRDFRSNPPKEIAGSKVKVVKDYDSL 503

Query: 502 KRTLLTESKEEAIDLP-KSNVLKYFLEDGSWFCLRPSGTEPKVKFYFAVKGS 552
           K T L   K   + +P  SNVL+YF EDG+   +RPSGTEPK+KFY  V+G+
Sbjct: 504 KMTDLDSGKVSDLIMPATSNVLQYFTEDGTKISVRPSGTEPKIKFYIEVRGA 555


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: 846
Number of extensions: 34
Number of successful extensions: 6
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: 582
Length adjustment: 36
Effective length of query: 545
Effective length of database: 546
Effective search space:   297570
Effective search space used:   297570
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