Alignments for a candidate for gadh1 in Lentibacillus jeotgali Grbi

GapMind for catabolism of small carbon sources

Alignments for a candidate for gadh1 in Lentibacillus jeotgali Grbi

Align D-gluconate dehydrogenase dehydrogenase subunit (EC 1.1.99.3) (characterized)
to candidate WP_010529735.1 ON01_RS04135 GMC family oxidoreductase

Query= metacyc::MONOMER-12745
         (594 letters)



>NCBI__GCF_000224785.1:WP_010529735.1
          Length = 578

 Score =  493 bits (1268), Expect = e-143
 Identities = 253/594 (42%), Positives = 366/594 (61%), Gaps = 25/594 (4%)

Query: 1   MATVMKKVDAVIVGFGWTGAIMAKELTEAGLNVLALERGPMQDTYPDGNYPQVIDELTYS 60
           M   + KVD V VG GW G I+A E+ +AG+ V+ LERG  + T    ++  V DE  Y+
Sbjct: 1   MVKKLDKVDVVTVGVGWAGGIIASEVAKAGVKVVGLERGDDRSTE---DFQMVHDEYRYA 57

Query: 61  VRKKLFQDISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELRM 120
           +R +L QD+S+ET+T R+++++ ALP RQ GAFL G GVGGAG+HW+G  +   P + ++
Sbjct: 58  IRYELMQDLSQETITFRNNLDERALPMRQFGAFLIGTGVGGAGVHWNGDTWFFAPYDFQI 117

Query: 121 RSHYEERYGKNFIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVRGQLVGDGKGG 180
           ++  +E+YGKN +P++ T+QD+G++Y+ELEP++   EK+ GTSG+               
Sbjct: 118 KTMTDEKYGKNKLPEEYTLQDWGITYDELEPYYRKFEKMAGTSGEP-------------- 163

Query: 181 NPYAPDRSDHFPLESQKNTYSAQLFQKAANDVGYKPYNLPSANTSGPYTNPYGAQMGPCN 240
           NP  P+R++ +P    K+T     + +AA ++G  P+  PSAN S  YTNP G  +  C 
Sbjct: 164 NPLRPERTEEYPTPPMKSTPILDQYMEAAKNLGLHPFRQPSANISEQYTNPDGQTLNQCQ 223

Query: 241 FCGFCSGYVCYMYSKASPNVNILPALKPLPNFELRPNSHVLRVNLDSSKTRATGVTYVDG 300
           +CGFC  + C   +K+ P V ++P  +   NFELR NS+V  +  D +K  ATGV YVD 
Sbjct: 224 YCGFCEKFGCEYGAKSDPTVTVIPTAQKTGNFELRTNSYVTGITHDGNK--ATGVRYVDV 281

Query: 301 Q-GREIEQPADLVILGAFQFHNVRLMLLSGIGKPYDPITGEGVVGKNFAYQNMATIKAYF 359
           Q G E EQPAD+V L ++  +N RL+L S +G+PYDP TG+GV+GKN+ YQ  A    +F
Sbjct: 282 QTGEEFEQPADVVALTSYTLNNCRLLLQSNLGRPYDPSTGKGVIGKNYCYQITAIATGFF 341

Query: 360 DKDVHTNNFIGAGGNGVAVDDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTP 419
            KD + N  +GAG  G  +DD+N DNFDH    F+ G  + + Q G RPI   + P   P
Sbjct: 342 -KD-NFNAAMGAGSLGTTLDDYNNDNFDHSDLDFIHGGSITMKQLGKRPINENAVPGDIP 399

Query: 420 AWGSAWKKATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYGLPLLRMTFDWQENDI 479
            WG  +K+ +  ++   + + + GA   ++ NYL LDP Y+D++G PLLRMT+D+ E D 
Sbjct: 400 RWGKKFKQESIKWFNRSIPVTSQGASMPHKNNYLSLDPTYKDSFGNPLLRMTYDFTEQDH 459

Query: 480 KMNRFMVEKMGKIAEAMNPKAIALLGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSALNR 539
            +  ++  +  +I E M  + +    K++ +HF+    Q  H+ GG IMG DP+TSALN 
Sbjct: 460 ALYEYITARCAEILEEMGAEVVE--PKELTDHFDIVPSQNDHITGGVIMGEDPETSALNN 517

Query: 540 YLQSWDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQ 593
           YLQ WDV NVFV GASAF    GYNPTG V AL Y +A  I  +Y K  G LV+
Sbjct: 518 YLQMWDVDNVFVIGASAFAHNGGYNPTGTVGALAYRAAEGIL-KYRKEKGQLVK 570


Lambda     K      H
   0.318    0.136    0.423 

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: 1081
Number of extensions: 64
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: 594
Length of database: 578
Length adjustment: 37
Effective length of query: 557
Effective length of database: 541
Effective search space:   301337
Effective search space used:   301337
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 24 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 2024 update 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