GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Methanobacterium veterum MK4

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_048080684.1 EJ01_RS13355 PQQ-dependent sugar dehydrogenase

Query= BRENDA::Q8ZUN8
         (371 letters)



>NCBI__GCF_000745485.1:WP_048080684.1
          Length = 347

 Score =  250 bits (638), Expect = 5e-71
 Identities = 147/368 (39%), Positives = 218/368 (59%), Gaps = 27/368 (7%)

Query: 1   MRRRTFLTLAVLVSLSASLGLLTAL--IRKGPSEEWKFKISEVASDLEVPWSIAPLGGGR 58
           M+R+T     V++ +   L +++AL  I   P+ +  ++   +  DL  PW+I  L  G+
Sbjct: 1   MKRKT-----VIIIIFVFLIIISALYFIIPKPANQQGYETEILVQDLNTPWAIDFLPDGK 55

Query: 59  YLVTERPGRLVLISPSGKKLVASFDVANVGEAGLLGLALHPEFPKKSWVYLYASYFAEGG 118
            + TER GR+ +      K V +  V  +GE+G+LG+A+ PEF    ++YLY  Y    G
Sbjct: 56  MIFTERDGRVSIFDNGTTKTVGTITVTQIGESGMLGIAVDPEFNTNKFIYLY--YTGANG 113

Query: 119 HIRNRVIRGRLDGSTFKLKEVKTLIDGIPGAYIHNGGRIRFGPDGMLYITTGDAADPRLA 178
              NR+ R  L+G+   LK    LID IP A  HNGGR++FG DG LY TTGDA + + A
Sbjct: 114 ---NRISRFTLNGT---LKNETVLIDRIPNAQFHNGGRLKFGSDGKLYATTGDATNNQSA 167

Query: 179 QDLSSLAGKILRVDEEGRPPADNPFPNSPIWSYGHRNPQGIDWHRASGVMVATEHGPVGH 238
           QD++SL GKILRV+++G  P+DNPF N  +++YG R+PQGI W   +  M  ++HG   +
Sbjct: 168 QDINSLGGKILRVNKDGTVPSDNPFRNY-VYAYGLRDPQGITWDPLTKEMYLSDHGATRN 226

Query: 239 DEVNIILKGGNYGWPLATGKAGRGEFVDPVIDTGSETWAPSGASFVHGDMFPGLRGWLLI 298
           DE+NII KGGNYGWP+  G      ++ P+      T APSG ++ +G ++        +
Sbjct: 227 DEINIITKGGNYGWPIYQGNESAQGYIKPLSVYTDFTLAPSGIAYYNGALY--------V 278

Query: 299 ACLRGSMLAAVNFG-DNMEVRKISTFFKNVFGRLRDVVIDDDGGILISTSNRDGRGSLRA 357
           A LRGS L  +    +   V      F ++ GR+R+VV+  DG + I+TSNRDGRG  ++
Sbjct: 279 AGLRGSQLRKITLSIEGNSVTGQEALFTSL-GRIREVVV-HDGYMYIATSNRDGRGVPQS 336

Query: 358 GDDKILKI 365
           GDDKI++I
Sbjct: 337 GDDKIIRI 344


Lambda     K      H
   0.320    0.140    0.432 

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: 357
Number of extensions: 22
Number of successful extensions: 4
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: 371
Length of database: 347
Length adjustment: 29
Effective length of query: 342
Effective length of database: 318
Effective search space:   108756
Effective search space used:   108756
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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