GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SMc00110
          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:

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