GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gdh in Sinorhizobium meliloti 1021

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate SMc00110 SMc00110 glucose dehydrogenase

Query= BRENDA::D4P700
         (796 letters)



>lcl|FitnessBrowser__Smeli:SMc00110 SMc00110 glucose dehydrogenase
          Length = 777

 Score =  791 bits (2042), Expect = 0.0
 Identities = 396/790 (50%), Positives = 512/790 (64%), Gaps = 20/790 (2%)

Query: 10  VVRFLTVLFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYAL 69
           V+    V+FAV+ G  +  GG  L  +GGS YY+I G   LLTAFLL+RR +AAL VYAL
Sbjct: 2   VIVLTAVVFAVI-GLALCGGGTRLLLLGGSPYYLIAGLGFLLTAFLLFRRRAAALWVYAL 60

Query: 70  LLLATLAWGVWEVGTDFWALAPRTDVLVIFGVWLVLPFVYR--GLYQPGKGALGAMG--V 125
           ++L +LAW +WEVG D+W L PR  V+++ G+WL+ P++ R  G   P     GA    +
Sbjct: 61  VVLGSLAWAIWEVGFDWWQLGPRGGVIILLGLWLLTPWIRRPLGFVSPTGEQYGASAWPL 120

Query: 126 ALVA--SAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQQGTRFS 183
           ALV+  S  V  YS+  DP  + G LP     A  A    N+  G+W  Y R   G R+S
Sbjct: 121 ALVSLLSVGVALYSMTQDPHDIRGDLPGEV--AANANLGGNVPPGEWHQYGRTPFGQRYS 178

Query: 184 PLKQINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALDA 243
           PL QI  +NV  LQVAWQ+QTGD+K P D  E T +VTP+K++DTLY+CTPH    ALDA
Sbjct: 179 PLDQIRPENVANLQVAWQYQTGDVKLPEDVSETTYQVTPLKVKDTLYVCTPHNWAIALDA 238

Query: 244 ATGKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKDASNTQPALCSRRIYLPVNDGRLF 303
           ATG++KWK+D     NP  QH TCRGV+Y   PAA   S      C+ R+YLP +D RL 
Sbjct: 239 ATGQEKWKYDSNSGMNPDRQHQTCRGVTYWADPAAAPGSP-----CAERVYLPTSDARLI 293

Query: 304 ALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAGAVTDNFSTRE 363
           ALDA  GE C +F +NG L L+        G Y  TSPPV     +++ GAV DN+ST E
Sbjct: 294 ALDATNGEVCTSFADNGVLHLEQGMKHNPAGYYYSTSPPVAVGDRLIIGGAVNDNYSTTE 353

Query: 364 PSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYDPKLDIVYLPM 423
            SG IR F++NTG L+W +D G  D  A      T+T NSPNSW+   YD  L +VY+PM
Sbjct: 354 QSGVIRAFNINTGALIWNWDSGNPDVTAPLPPGQTYTTNSPNSWSVFSYDEGLGLVYIPM 413

Query: 424 GVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQPTLADITD 483
           G   PD  G  R+   E+Y+SS++AL+  TG + W  QTVHHDLWDMD+P+QP L DIT 
Sbjct: 414 GNQVPDQLGMGRSEHVEKYSSSIVALDINTGAVRWVRQTVHHDLWDMDVPAQPALLDITR 473

Query: 484 KDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAKGDHVSATQPYSELTFRP 543
           +DG  VP +  P K G+I+VLDRR+G+ ++P  E P P GA   D  + TQP S LTF P
Sbjct: 474 EDGTVVPALVGPTKQGDIYVLDRRSGEPIIPIEEVPAPGGAIPEDFTAPTQPVSGLTFMP 533

Query: 544 KQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLGMFEWGGISVDP 603
              L ++DMWG +M+DQL CR+ F+ L+YEG +TPPS +GT+V+PGN G F WG ++VDP
Sbjct: 534 PP-LMERDMWGISMFDQLACRIEFRTLKYEGRYTPPSLEGTIVYPGNFGTFNWGSVAVDP 592

Query: 604 HRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGIQPQYGVPYGVELNPFLS 663
            RQ+    P  L F S+L+PR     +  PKG  G  G+E G+    G PYGV + PFL 
Sbjct: 593 ERQVMFGMPTYLAFTSRLVPR----DQIAPKG-EGEKGSEQGLNRNEGAPYGVFMGPFLG 647

Query: 664 PFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPLPFKMGMPMLGGPVATAGKV 723
           P G+PC+ P WGYV+  DL+T ++ +K + GTV D +P+PLPFK+G+P +GGP+ T G +
Sbjct: 648 PLGIPCQAPPWGYVAGADLRTGKIAYKHKNGTVYDMTPLPLPFKLGVPGIGGPMITKGGL 707

Query: 724 FFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTYEVNGKQYVVIAAGGHGSFGTKL 783
            F+GA  D+Y RA+   TGE LW+ARLPAGGQ+TPMTY V  KQYV+I AGGHGS GTK 
Sbjct: 708 AFLGAAVDDYFRAYDLTTGEQLWEARLPAGGQSTPMTYTVGEKQYVLIVAGGHGSVGTKP 767

Query: 784 GDYVIAYALP 793
           GDYVIAY LP
Sbjct: 768 GDYVIAYTLP 777


Lambda     K      H
   0.319    0.137    0.433 

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: 2303
Number of extensions: 166
Number of successful extensions: 12
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 796
Length of database: 777
Length adjustment: 41
Effective length of query: 755
Effective length of database: 736
Effective search space:   555680
Effective search space used:   555680
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: 55 (25.8 bits)

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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