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 lactose 3-dehydrogenase flavin subunit (EC 1.1.99.13) (characterized)
to candidate Echvi_1044 Echvi_1044 Choline dehydrogenase and related flavoproteins

Query= metacyc::MONOMER-15712
         (579 letters)



>FitnessBrowser__Cola:Echvi_1044
          Length = 566

 Score =  533 bits (1372), Expect = e-155
 Identities = 269/572 (47%), Positives = 366/572 (63%), Gaps = 9/572 (1%)

Query: 1   MANLNGRARRKNTYDAIVVGSGITGGIAAKELTEKGLKVLVLERGPMVRHLEDYPTAMLD 60
           MANLN + + +N++ AIV+GSG++GG AAKEL +KG+K LVLERG  V H +DYPT  + 
Sbjct: 1   MANLNIKGKEENSFGAIVIGSGMSGGFAAKELCDKGVKTLVLERGRSVVHNKDYPTTNMM 60

Query: 61  PWQSKYPQGKLPEAELNAHYKVQRRTGYTMTEQTQHFFVRDDEHPYTEENRFDWIRGYHV 120
           PW+ ++ +G++PE     +  V R   Y   E   HFFV+D EHPY +E  FDWIRGY  
Sbjct: 61  PWEFEH-RGQIPEDIQRENPVVSRC--YAFREDAAHFFVKDQEHPYIQEKPFDWIRGYQT 117

Query: 121 GGRSLTWGRQSYRHSPIDFEANAREGIAVDWPIRYEDLAPWYEHVERFIGVSGQAEGLPH 180
           GG+SL W RQ  R S  DFE  AR+G AVDWPIRY+DLAPWY +VE+F+GV+G  +G+PH
Sbjct: 118 GGKSLLWARQVQRWSDHDFEGPARDGFAVDWPIRYKDLAPWYSYVEKFVGVAGFHDGIPH 177

Query: 181 FPDGHYQPPMELNCVEKAFKARSEARFPERRVTIGRTAHLTDPTEEQLALGRTKCQYRNL 240
            PDG + P +EL   E+ FK+  E ++P R V  GR AH+T   E     GR  CQ+R +
Sbjct: 178 LPDGEFLPGIELTAAEEYFKSVVEEKYPGRNVISGRYAHITGNAEYYAKQGRGICQHRTI 237

Query: 241 CIRGCPFGAYYSSNSGGLIAAERTGNLVIRPNSIVTELIYDERAGRASGVRILDAETRKD 300
           C RGCPFG Y+SSNS  L  A+RTGNL ++ +++V  +IYD+   +A+GVR++DA T++ 
Sbjct: 238 CQRGCPFGGYFSSNSASLPWAQRTGNLTLKNHAVVHSIIYDDTQQKATGVRVIDANTKEV 297

Query: 301 EEFHADVIFLCASALNSAWIMMNSTSSRFPNGFGNASDQLGRNVMDHHLGAGATGQAPEF 360
            E++A +IF+ ASALN+  I++NSTS RFP+G GN +  +G+ +  H+   G +G+    
Sbjct: 298 TEYYAPIIFVNASALNTNLILLNSTSKRFPHGLGNDNGLMGKFIAFHNYRGGVSGEYEGL 357

Query: 361 ADMYFSGRRPNGIYVPRFRNLGDAASKRSDYLRGFGYQGGAGRATWERDRGQGGRGFGAA 420
                 G+RP   Y+PRFRN+    +K   +LR  GY  G    T  +D    G G    
Sbjct: 358 KSFTTEGKRPTSGYMPRFRNVDKQETK---FLR--GYAAGI-HGTRSKDVDYSGTGADLV 411

Query: 421 RKAALSQPGPWTMGLSGFGEMLPYADNRVTLNRDVEDKFGLPTLTMNVTMRDNEMAMRRD 480
           +       GPW +G    GE +P   N V L+   +D++ +P L +NV    N++ M +D
Sbjct: 412 KNIMNPSYGPWRIGSHMMGETIPKESNYVALDTAQKDEWDMPQLKVNVDYDQNDLDMIKD 471

Query: 481 MQAAAAEMLEAAGFQNVRAHDNGFAPGLGIHEMGTARMGRDPKTSVLNAHNQVHECKNVY 540
            +   AEM +AAGF+N+R  D+   PGL IHEMG  RMG DPKTS+LN H+Q+H C NVY
Sbjct: 472 YREQLAEMFDAAGFKNIRTWDDERRPGLDIHEMGGVRMGHDPKTSLLNKHHQLHACPNVY 531

Query: 541 VTDGAAMASASCVNPSLTYMALTARAADHAVR 572
           VTDGA M S S  NPSLTYM   ARA DHA++
Sbjct: 532 VTDGACMTSTSTQNPSLTYMVFAARAVDHALK 563


Lambda     K      H
   0.319    0.135    0.414 

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: 911
Number of extensions: 36
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: 579
Length of database: 566
Length adjustment: 36
Effective length of query: 543
Effective length of database: 530
Effective search space:   287790
Effective search space used:   287790
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 (21.8 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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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