Alignments for a candidate for sdh in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdh in Sinorhizobium meliloti 1021

Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate SMc00110 SMc00110 glucose dehydrogenase

Query= BRENDA::Q70JN9
         (743 letters)



>FitnessBrowser__Smeli:SMc00110
          Length = 777

 Score =  477 bits (1228), Expect = e-139
 Identities = 262/665 (39%), Positives = 368/665 (55%), Gaps = 34/665 (5%)

Query: 86  SMDPNDVPQMAPQQSASPAS-------GDWAAYGHDDSQMRYSPLSEITPQNADQLKVAF 138
           + DP+D+    P + A+ A+       G+W  YG      RYSPL +I P+N   L+VA+
Sbjct: 136 TQDPHDIRGDLPGEVAANANLGGNVPPGEWHQYGRTPFGQRYSPLDQIRPENVANLQVAW 195

Query: 139 VYHTGSYPRPGQTNKWAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEA 198
            Y TG    P   ++   + TP+KV D LY+C+  N  + +D ATG+E W+++ N     
Sbjct: 196 QYQTGDVKLPEDVSETTYQVTPLKVKDTLYVCTPHNWAIALDAATGQEKWKYDSNSGMNP 255

Query: 199 IPYTAACKGVTYFTSSQVPEGQPCHNRILEGTLDMRLIAVDAATGNLCEGFGNGGQVNLM 258
                 C+GVTY+       G PC  R+   T D RLIA+DA  G +C  F + G ++L 
Sbjct: 256 DRQHQTCRGVTYWADPAAAPGSPCAERVYLPTSDARLIALDATNGEVCTSFADNGVLHLE 315

Query: 259 QGLGESVPGFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGKFLWAWDVN 318
           QG+  +  G+   T+PP  V   +++   V D       SGVIR ++  +G  +W WD  
Sbjct: 316 QGMKHNPAGYYYSTSPPVAVGDRLIIGGAVNDNYSTTEQSGVIRAFNINTGALIWNWDSG 375

Query: 319 RPNDHSQPTGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSALRSPEENKVSSA 378
            P+  +       Y+  +PNSW+  + D  LGLVY+P GN   D     RS    K SS+
Sbjct: 376 NPDVTAPLPPGQTYTTNSPNSWSVFSYDEGLGLVYIPMGNQVPDQLGMGRSEHVEKYSSS 435

Query: 379 VVALDVKTGSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPVPALIMPTKRGQTFVLD 438
           +VALD+ TG+ RWV QTVH D+WD D+ +Q  L+D+  +DG  VPAL+ PTK+G  +VLD
Sbjct: 436 IVALDINTGAVRWVRQTVHHDLWDMDVPAQPALLDITREDGTVVPALVGPTKQGDIYVLD 495

Query: 439 RRDGKPILPVEERPAPSPGVIPGDPRSPTQPWS--TGMPALRVPDLKETDMWGMSPIDQL 496
           RR G+PI+P+EE PAP  G IP D  +PTQP S  T MP    P L E DMWG+S  DQL
Sbjct: 496 RRSGEPIIPIEEVPAPG-GAIPEDFTAPTQPVSGLTFMP----PPLMERDMWGISMFDQL 550

Query: 497 FCRIKFRRANYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSGILIANWNITPMYDQ 556
            CRI+FR   Y G +TPPS++   I YPG  G  +WGSV+ DP+  ++       P Y  
Sbjct: 551 ACRIEFRTLKYEGRYTPPSLEGT-IVYPGNFGTFNWGSVAVDPERQVMFG----MPTYLA 605

Query: 557 LVTRKKADELGLMPIDD--PNYKPGGGGAEGNGAMDGTPYGIVVTPFWDQYTGMMCNRPP 614
             +R       L+P D   P  +   G  +G    +G PYG+ + PF     G+ C  PP
Sbjct: 606 FTSR-------LVPRDQIAPKGEGEKGSEQGLNRNEGAPYGVFMGPFLGP-LGIPCQAPP 657

Query: 615 YGMITAIDMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVFIAA 674
           +G +   D++ G K+ ++H  GT     P  LP  LP+++G P  GG ++T GG+ F+ A
Sbjct: 658 WGYVAGADLRTG-KIAYKHKNGTVYDMTP--LP--LPFKLGVPGIGGPMITKGGLAFLGA 712

Query: 675 ATDNQIRAIDEHTGKVVWSAVLPGGGQANPMTYEANGHQYVAIMAGGHHFMMTPVSDQLV 734
           A D+  RA D  TG+ +W A LP GGQ+ PMTY     QYV I+AGGH  + T   D ++
Sbjct: 713 AVDDYFRAYDLTTGEQLWEARLPAGGQSTPMTYTVGEKQYVLIVAGGHGSVGTKPGDYVI 772

Query: 735 VYALP 739
            Y LP
Sbjct: 773 AYTLP 777


Lambda     K      H
   0.315    0.134    0.428 

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: 2199
Number of extensions: 165
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: 743
Length of database: 777
Length adjustment: 40
Effective length of query: 703
Effective length of database: 737
Effective search space:   518111
Effective search space used:   518111
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: 42 (22.0 bits)
S2: 55 (25.8 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources