Alignments for a candidate for etoh-dh-c in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for etoh-dh-c in Sinorhizobium meliloti 1021

Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate SMc00110 SMc00110 glucose dehydrogenase

Query= BRENDA::D2SZY4
         (742 letters)



>FitnessBrowser__Smeli:SMc00110
          Length = 777

 Score =  136 bits (343), Expect = 4e-36
 Identities = 185/706 (26%), Positives = 265/706 (37%), Gaps = 144/706 (20%)

Query: 5   ASAKRRSLLGILAAGTICAAALPYAAVPARADGQGNTG-EAIIHADDHPENWLSYGRTYS 63
           ASA   +L+ +L+ G +   ++       R D  G     A +  +  P  W  YGRT  
Sbjct: 115 ASAWPLALVSLLSVG-VALYSMTQDPHDIRGDLPGEVAANANLGGNVPPGEWHQYGRTPF 173

Query: 64  EQRYSPLDQINRSNVGDLKLAWYYTLD--------TNRGQEATPLVVDGIMYATTNWSKM 115
            QRYSPLDQI   NV +L++AW Y           +    + TPL V   +Y  T  +  
Sbjct: 174 GQRYSPLDQIRPENVANLQVAWQYQTGDVKLPEDVSETTYQVTPLKVKDTLYVCTPHNWA 233

Query: 116 EALDAATGKLLWQYDPKVPGNIADKGCCDTVNRGAGYWNG-----------KVFWGTFDG 164
            ALDAATG+  W+YD    G   D+       RG  YW             +V+  T D 
Sbjct: 234 IALDAATGQEKWKYDSN-SGMNPDRQ--HQTCRGVTYWADPAAAPGSPCAERVYLPTSDA 290

Query: 165 RLVAADAKTGKKVWEVNTIPADASL-----GKQRS-----YTVDGAVRVAKGLVLIGNGG 214
           RL+A DA  G    EV T  AD  +     G + +     Y+    V V   L++ G   
Sbjct: 291 RLIALDATNG----EVCTSFADNGVLHLEQGMKHNPAGYYYSTSPPVAVGDRLIIGGAVN 346

Query: 215 AEFGA---RGFVSAFDAETGKLKWRFYTVPNNKNEPDHAASDNILMNKAYKTWGPKGAWV 271
             +      G + AF+  TG L W +     +   PD  A   +   + Y T  P     
Sbjct: 347 DNYSTTEQSGVIRAFNINTGALIWNW-----DSGNPDVTAP--LPPGQTYTTNSPNS--- 396

Query: 272 RQGGGGTVWDSLVYDPVSDLIYLAVGNGSPWNYKY-RSEGIGSNLFLGSIVALKPETGEY 330
                   W    YD    L+Y+ +GN  P      RSE +    +  SIVAL   TG  
Sbjct: 397 --------WSVFSYDEGLGLVYIPMGNQVPDQLGMGRSEHV--EKYSSSIVALDINTGAV 446

Query: 331 VWHFQATPMDQWDYTSVQQIMTLDMP-VNGEMRHVIVHAPKNGFFYVLDAKTGEFL---- 385
            W  Q    D WD     Q   LD+   +G +   +V   K G  YVLD ++GE +    
Sbjct: 447 RWVRQTVHHDLWDMDVPAQPALLDITREDGTVVPALVGPTKQGDIYVLDRRSGEPIIPIE 506

Query: 386 ---SGKNYVYQNWANGLDPLTGRPIYNP---------------------------DGLYT 415
              +    + +++     P++G     P                           +G YT
Sbjct: 507 EVPAPGGAIPEDFTAPTQPVSGLTFMPPPLMERDMWGISMFDQLACRIEFRTLKYEGRYT 566

Query: 416 ---LNGKFWYGIPGPLGAHNFMAMAYSPKTHLVY------------IPAHQIP---FGYK 457
              L G   Y  PG  G  N+ ++A  P+  +++            +P  QI     G K
Sbjct: 567 PPSLEGTIVY--PGNFGTFNWGSVAVDPERQVMFGMPTYLAFTSRLVPRDQIAPKGEGEK 624

Query: 458 NQVGGFK------------PHADSWNVGLDMTKNGLPDTPEARTAYIKDLHGWLLAWDPV 505
               G              P      +       G     + RT  I   H     +D  
Sbjct: 625 GSEQGLNRNEGAPYGVFMGPFLGPLGIPCQAPPWGYVAGADLRTGKIAYKHKNGTVYDMT 684

Query: 506 KMETVWKIDHKGPWNGGILATGGDLLFQGLA-NGEFHAYDATNGSDLYKFDAQSGIIAPP 564
            +   +K+    P  GG + T G L F G A +  F AYD T G  L++    +G  + P
Sbjct: 685 PLPLPFKLG--VPGIGGPMITKGGLAFLGAAVDDYFRAYDLTTGEQLWEARLPAGGQSTP 742

Query: 565 MTYSVNGKQYVAVEVGWGGIYPISMGGVGRTSGWTVNHSYIAAFSL 610
           MTY+V  KQYV +  G         G VG   G      Y+ A++L
Sbjct: 743 MTYTVGEKQYVLIVAG-------GHGSVGTKPG-----DYVIAYTL 776


Lambda     K      H
   0.318    0.137    0.441 

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: 2090
Number of extensions: 157
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 2
Length of query: 742
Length of database: 777
Length adjustment: 40
Effective length of query: 702
Effective length of database: 737
Effective search space:   517374
Effective search space used:   517374
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 (21.7 bits)
S2: 55 (25.8 bits)

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

Downloads

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

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:

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