GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Nocardiopsis gilva YIM 90087

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_051060823.1 CDO52_RS21155 phospho-sugar mutase

Query= BRENDA::C6L2F4
         (596 letters)



>NCBI__GCF_002263495.1:WP_051060823.1
          Length = 559

 Score =  284 bits (726), Expect = 8e-81
 Identities = 213/563 (37%), Positives = 273/563 (48%), Gaps = 63/563 (11%)

Query: 12  ALEAAVNFWRSVDRREETQKETLELLKNLTEDELAKLFLARLEFGTAGLRGRMGAGFSRM 71
           +L      W   D    T+ E   +L    +  LA+ F ARLEFGTAGLRG +GAG +RM
Sbjct: 12  SLRGQAEAWLEQDPDPRTRDELKAILDAGDDAALAERFGARLEFGTAGLRGALGAGPNRM 71

Query: 72  NDVTIQQTTQGYCAFLVDVFGEDGKDRGVVIGFDARHNSRRFAQLTAAVFLSKGFRVQLF 131
           N VT+ +   G   +L       G  R VVIG+DARH S  FA+ TAAV    G    L 
Sbjct: 72  NRVTVMRAAAGVARWL-------GSGRCVVIGYDARHRSADFAEDTAAVLTGAGCTALLL 124

Query: 132 SDIVHTPMVPYTVVAANCIAGIMITASHNPKADNGYKVYAAN-----GAQIIPPMDSEIS 186
              + TP++ Y V A    AGIM+TASHNP  DNGYKVY        G+QI+ P+D+EIS
Sbjct: 125 PRPLPTPVLAYAVRALGADAGIMVTASHNPPQDNGYKVYMGGEGPGAGSQIVAPVDAEIS 184

Query: 187 AFINSNLDFWSDVDEYFDSKTGMLTEKAANSSLLEDPLNTYVDAYIKDIAADLCVAEQQG 246
           A I++                G ++E    S        T VD  I +       A   G
Sbjct: 185 AAIDA---------------VGPVSELKVGSGW------TVVDEEIVERYLGAITAVPLG 223

Query: 247 SD--LKFMYTAMHGVGTPMVKKMLAAFGFNDNLLTVDAQCTPDPEFPTVAFPNPEEKGAL 304
           SD  +   YT +HGVG   ++      GF    L V  Q  PDP+FPTVAFPNPEE GA+
Sbjct: 224 SDRAVSVTYTPLHGVGASTLRAAFERVGFPAPRL-VPEQAEPDPDFPTVAFPNPEEPGAM 282

Query: 305 DLAFQEADSHGLTLVIANDPDADRFAAAEKCDGRWYQFTGDELGAILGAYAIKLREGQGI 364
           DLA     ++G  LV+ANDPDADR A A    G     TGDE+G +L  Y ++   G   
Sbjct: 283 DLALAVGRANGSDLVVANDPDADRVAVAVPGHG---LLTGDEIGGLLAEYILRHTAG--- 336

Query: 365 SKSKMALICSAVSSRMLQKIAKENGCTFAETMTGFKWMENKAIEMEAEGLIPVFVYEEAL 424
                 +  + VS+ +L KIA + G    ET+TGFKW+          G   VF YEEAL
Sbjct: 337 --GDRVVATTIVSAGLLPKIAADYGVRCVETLTGFKWLARAG----GPGERNVFSYEEAL 390

Query: 425 GYAL----SQRVRDKDGVSAAAVWMQMAIDL-YSRGQTVMDFLMSLRKRYGYFVTRNSYF 479
           GY L    S+ V DKDG+SAA     MA +     G+T++D L    +RYG   T     
Sbjct: 391 GYCLGGDTSRPVADKDGISAALAVAAMAAEAKRDGGRTLLDLLDDQARRYGLHRTAQVAV 450

Query: 480 ICPDPRLIQGLFKDFANGGNYPKQLGPFTIRRIRDVGRGYDSEEQCSFPSNCEMLTVYLD 539
              D  L+    +        P+  G   +  I D   G     +   P+  + L   L 
Sbjct: 451 RVSDLALLADTMRRLR--AEPPRAFGSLEVEAIEDFAEG-----RGDLPAT-DALRYRLG 502

Query: 540 N--GAVVTLRGSGTEPKLKYYAE 560
               A +TLR SGTEPKLK Y E
Sbjct: 503 GPARARITLRPSGTEPKLKAYLE 525


Lambda     K      H
   0.320    0.135    0.398 

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: 833
Number of extensions: 45
Number of successful extensions: 10
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: 596
Length of database: 559
Length adjustment: 36
Effective length of query: 560
Effective length of database: 523
Effective search space:   292880
Effective search space used:   292880
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 (21.8 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