GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Magnetospirillum magneticum AMB-1

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_011383017.1 AMB_RS02970 alpha-D-glucose phosphate-specific phosphoglucomutase

Query= BRENDA::Q9SCY0
         (623 letters)



>NCBI__GCF_000009985.1:WP_011383017.1
          Length = 542

 Score =  640 bits (1652), Expect = 0.0
 Identities = 319/555 (57%), Positives = 405/555 (72%), Gaps = 16/555 (2%)

Query: 69  IKSLPTKPIEGQKTGTSGLRKKVKVFMEDNYLANWIQALFNSLPLEDYKNATLVLGGDGR 128
           +K++PT P  GQK GTSGLRKKVKVF + +YL N++QA+F+S+   D    TLV+GGDGR
Sbjct: 4   VKTIPTTPFSGQKPGTSGLRKKVKVFAQPHYLENFVQAVFDSIG--DLGGKTLVVGGDGR 61

Query: 129 YFNKEASQIIIKIAAGNGVGQILVGKEGILSTPAVSAVIRKRKANGGFIMSASHNPGGPE 188
           Y N+ A Q I+K+AA +G  +++VG+ GILSTPA S VIRK K  GG I+SASHNPGGP+
Sbjct: 62  YHNRTAIQTILKMAAASGFAKVMVGRGGILSTPAASCVIRKYKTFGGIILSASHNPGGPD 121

Query: 189 YDWGIKFNYSSGQPAPETITDKIYGNTLSISEIKVAEIPDIDLSQVGVTKYGNFSVEVID 248
            D+GIK+N  +G PAPE IT+ IY  T  IS  K+ E  D+DL  +G    G  +V+V D
Sbjct: 122 EDFGIKYNIPAGGPAPEAITEAIYARTQEISSYKIIEAADVDLDTIGERGLGGMTVQVFD 181

Query: 249 PVSDYLELMEDVFDFDLIRGLLSRSDFGFMFDAMHAVTGAYAKPIFVDNLGAKPDSISNG 308
           PV+DY ELME +FDF  IR   + + F   FDAMHAVTG YA  I  + LGA   ++ NG
Sbjct: 182 PVADYAELMESLFDFGAIRAAFA-AGFRMKFDAMHAVTGPYATEILENRLGAPKGTVMNG 240

Query: 309 VPLEDFGHGHPDPNLTYAKDLVDVMYRDNGPDFGAASDGDGDRNMVLGNKFFVTPSDSVA 368
           VPLEDFGHGHPDPNL +A DLV+ +     PDFGAASDGDGDRNM+LG  F+VTPSDS+A
Sbjct: 241 VPLEDFGHGHPDPNLVHAHDLVEALTGAGAPDFGAASDGDGDRNMILGRDFYVTPSDSLA 300

Query: 369 IIAANAQEAIPYFRAGPKGLARSMPTSGALDRVAEKLKLPFFEVPTGWKFFGNLMDAGKL 428
           ++AANA    P +  G KG+ARSMPTS A DRVA KL +P +E PTGWKFFG L+DAGK 
Sbjct: 301 VLAANA-TLCPGYARGLKGIARSMPTSAAPDRVAAKLGIPAWETPTGWKFFGTLLDAGKA 359

Query: 429 SICGEESFGTGSDHIREKDGIWAVLAWLSILAHRNKDTKPGDKLVSVADVVKEYWATYGR 488
           + CGEESFGTGSDH+REKDG+WAVLAWL++LA R +         SVAD+V  +W  YGR
Sbjct: 360 TFCGEESFGTGSDHVREKDGLWAVLAWLNVLAVRKQ---------SVADIVTAHWREYGR 410

Query: 489 NFFSRYDYEECESEGANKMIEYLREILSKSKAGDVYGNYVLQFADDFSYTDPVDGSVASK 548
           N +SR+DYE  +S  A  ++E+LR +   S  G+  G Y + F DDF+YTDPVDGSV+ K
Sbjct: 411 NVYSRHDYEGIDSAAAEGLMEHLRGL---SLKGERLGTYTVAFNDDFAYTDPVDGSVSKK 467

Query: 549 QGVRFVFTDGSRIIFRLSGTGSAGATVRIYIEQFEPDVSKHDVDAQIALKPLIDLALSVS 608
           QG+R VF DGSR++FRLSGTG+ GAT+R+YIE+FEPD +KH +D Q+AL  LI +A  ++
Sbjct: 468 QGIRVVFEDGSRVVFRLSGTGTEGATLRVYIERFEPDATKHHLDPQVALADLITIARDLA 527

Query: 609 KLKDFTGREKPTVIT 623
           +++  TGR +PTVIT
Sbjct: 528 QIEARTGRTEPTVIT 542


Lambda     K      H
   0.317    0.136    0.399 

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: 1002
Number of extensions: 44
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: 623
Length of database: 542
Length adjustment: 36
Effective length of query: 587
Effective length of database: 506
Effective search space:   297022
Effective search space used:   297022
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 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