Alignments for a candidate for lacA in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacA in Echinicola vietnamensis KMM 6221, DSM 17526

Align periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13) (characterized)
to candidate Echvi_1044 Echvi_1044 Choline dehydrogenase and related flavoproteins

Query= reanno::Pedo557:CA265_RS15345
         (567 letters)



>FitnessBrowser__Cola:Echvi_1044
          Length = 566

 Score =  523 bits (1346), Expect = e-152
 Identities = 262/569 (46%), Positives = 365/569 (64%), Gaps = 15/569 (2%)

Query: 1   MMNLNTNLKAENTYDAIVIGSGISGGWAAKELTEKGLRVLMLERGMNIEHITGYETAMKN 60
           M NLN   K EN++ AIVIGSG+SGG+AAKEL +KG++ L+LERG ++ H   Y T    
Sbjct: 1   MANLNIKGKEENSFGAIVIGSGMSGGFAAKELCDKGVKTLVLERGRSVVHNKDYPTTNMM 60

Query: 61  PWDFKHAGKLTEEQKRTHPVQKRDYPYQEANEKWWVNDLECPYTEDKRFDWYRGFHVGGK 120
           PW+F+H G++ E+ +R +PV  R Y ++E    ++V D E PY ++K FDW RG+  GGK
Sbjct: 61  PWEFEHRGQIPEDIQRENPVVSRCYAFREDAAHFFVKDQEHPYIQEKPFDWIRGYQTGGK 120

Query: 121 SLMWGRQSYRLSDHNFEDNARDGHGSDWPVRYAELSPWYDYAERFAGISGSKENWPTCPD 180
           SL+W RQ  R SDH+FE  ARDG   DWP+RY +L+PWY Y E+F G++G  +  P  PD
Sbjct: 121 SLLWARQVQRWSDHDFEGPARDGFAVDWPIRYKDLAPWYSYVEKFVGVAGFHDGIPHLPD 180

Query: 181 GQFLPPMDLNIVEKSVKARIEEHYKRERIMMIGRVANLT-----VPHKGRGNCQYRNLCS 235
           G+FLP ++L   E+  K+ +EE Y    ++  GR A++T        +GRG CQ+R +C 
Sbjct: 181 GEFLPGIELTAAEEYFKSVVEEKYPGRNVIS-GRYAHITGNAEYYAKQGRGICQHRTICQ 239

Query: 236 RGCPFGAYFSTQSSTLPAAMATKRLTLRPYSIVNHIIYDKDTKKAKGVMVIDAETNKTME 295
           RGCPFG YFS+ S++LP A  T  LTL+ +++V+ IIYD   +KA GV VIDA T +  E
Sbjct: 240 RGCPFGGYFSSNSASLPWAQRTGNLTLKNHAVVHSIIYDDTQQKATGVRVIDANTKEVTE 299

Query: 296 FYAKIVFVNGSTLGSTFVLLNSTSEAHPNGLGNGSGQLGHNLMDHHFRCGASGEAEGFDD 355
           +YA I+FVN S L +  +LLNSTS+  P+GLGN +G +G  +  H++R G SGE EG   
Sbjct: 300 YYAPIIFVNASALNTNLILLNSTSKRFPHGLGNDNGLMGKFIAFHNYRGGVSGEYEGLKS 359

Query: 356 KYTYGRRANGIYIPRYQNIGNDKRDYLRGF--GYQGGASRANWQGDVAELSFGADLKQKM 413
             T G+R    Y+PR++N+   +  +LRG+  G  G  S+     DV     GADL + +
Sbjct: 360 FTTEGKRPTSGYMPRFRNVDKQETKFLRGYAAGIHGTRSK-----DVDYSGTGADLVKNI 414

Query: 414 TTP--GKWSMGLGGFGEMLPYYENKVYIDKTKKDKWGQPVLAIDCEYKENEKKMRVDMMN 471
             P  G W +G    GE +P   N V +D  +KD+W  P L ++ +Y +N+  M  D   
Sbjct: 415 MNPSYGPWRIGSHMMGETIPKESNYVALDTAQKDEWDMPQLKVNVDYDQNDLDMIKDYRE 474

Query: 472 DAAEMLEKAGMKNIKTFDNGCYPGMAIHEMGTARMGNDPKTSVLNKWNQMHEVNNVFVTD 531
             AEM + AG KNI+T+D+   PG+ IHEMG  RMG+DPKTS+LNK +Q+H   NV+VTD
Sbjct: 475 QLAEMFDAAGFKNIRTWDDERRPGLDIHEMGGVRMGHDPKTSLLNKHHQLHACPNVYVTD 534

Query: 532 GSCMPSIACQNPSLTFMALTARACDYAVK 560
           G+CM S + QNPSLT+M   ARA D+A+K
Sbjct: 535 GACMTSTSTQNPSLTYMVFAARAVDHALK 563


Lambda     K      H
   0.317    0.134    0.421 

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: 1018
Number of extensions: 50
Number of successful extensions: 3
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: 567
Length of database: 566
Length adjustment: 36
Effective length of query: 531
Effective length of database: 530
Effective search space:   281430
Effective search space used:   281430
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: 53 (25.0 bits)

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

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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