Alignments for a candidate for aldA in Sulfurimonas denitrificans DSM 1251

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldA in Sulfurimonas denitrificans DSM 1251

Align bifunctional L-rhamnulose 1-phosphate aldolase/lactaldehyde dehydrogenase (EC 4.1.2.19; EC 1.2.1.22) (characterized)
to candidate WP_011373584.1 SUDEN_RS10225 bifunctional aldolase/short-chain dehydrogenase

Query= metacyc::BSU31220-MONOMER
         (689 letters)



>NCBI__GCF_000012965.1:WP_011373584.1
          Length = 653

 Score =  354 bits (908), Expect = e-102
 Identities = 222/686 (32%), Positives = 353/686 (51%), Gaps = 43/686 (6%)

Query: 2   VKHIWDSERAAQLPKGVEELVYRSNLIGSDRTVCNWGGGNTSMKTTEKDFRGREIEVMWV 61
           +K +WD++ A      ++  VY S L+G D ++   GGGNTS+K+T  +  G   E+++V
Sbjct: 1   MKSLWDNKEAQNYKTDLDLRVYTSRLLGRDSSLVLHGGGNTSVKSTATNLFGEVEEILYV 60

Query: 62  KGSGSDLATMKAHNFSGLKLDDIRPLIKRDQMPDEEMVDYLSHCMIDSKHPRPSIETLLH 121
           KGSG DLAT++A  F+ +K++ +  + +  ++ D +MV Y    M +   P PS+E +LH
Sbjct: 61  KGSGWDLATIEAEGFAPVKMEMLLKMAELKELSDTDMVKYQRLSMTNPSAPNPSVEAILH 120

Query: 122 AFLPYKHVDHTHPDAIISICCADNGKQIAEDIYGNRFVWVPYVRPGFTLSKMIAEGVANN 181
           A +P+K VDHTH DA+++I   + G+    +IYG+  + +PY+ PGF L+K++ E     
Sbjct: 121 AIIPFKFVDHTHTDAVVTITNTEGGEDKIREIYGDSVLVIPYIMPGFVLAKLVYEMTKEV 180

Query: 182 PHAEL--VLMEKHGLVTWGETSETCYQKTISIIQEAEQYINDRINQHEVFGGKRYQPLPE 239
             ++L  +++  HGL T+   ++  Y+KTI ++  AE+Y+ D   Q  V          E
Sbjct: 181 DWSKLEGMVLMNHGLFTFSNEAKESYEKTIELVDMAEKYLKDNGAQLHV----------E 230

Query: 240 DKRKQILAGIMPVIRGAVS--EEKKMILSYDDHDDVLEFVNSVQAPALSQIGAACPDHLV 297
                I    +  IR  VS  + K  I  ++D D  L F +      ++  G   PDH++
Sbjct: 231 KSSANIETLTLAKIRKEVSSLKGKATISIFNDSDLALHF-SKQNIDKIATQGPLTPDHVI 289

Query: 298 HTKRVPLYIDWNPETQDVHKLADLIKSGVETFTSEYQAYFTRNQQDGDQIFESAPRVILI 357
            TKR+P              L D  KS +  +   Y+ YF  N+ D + +   AP   ++
Sbjct: 290 RTKRIPSI------------LGDDFKSDLANYVKAYRDYFEANKTD-ETMLNPAPNYAIL 336

Query: 358 PGIGMVNTGKSYAMSKVSGALYRRAIAVMKGATALGQFVSLHENESYHVEYWPLELYKLT 417
            G G ++ G++   + +   +       +  A  LG + +L   + + V YW LE  KL 
Sbjct: 337 RGRGALSFGENAKDANIIKDINEHTYEAILRAEKLGGYRALSPAKIFEVGYWSLEQAKLK 396

Query: 418 LAPPEAEFSRKVALITGGAGGIGSAACRRFAAEGGHVIVADLNIEGAQKIAGEINDAYGK 477
                +EFS K+AL+TGGA GIG A  +   A G  V+  D+N         ++   + +
Sbjct: 397 SGAKASEFSGKIALVTGGASGIGLAIAKMLNARGAAVVALDIN--------PDVERIFNR 448

Query: 478 GRAMAVKMDVTKEEDVQSAFERAALAYGGIDIVVNNAGLAT-SSPFDETSLKEWNLNMNV 536
             A+ ++ D+T  +D+QSA  +   ++GGIDIVV+NAG+ T S   DE S + W  +M++
Sbjct: 449 ADAIGIRCDLTCSDDIQSAISKTVKSFGGIDIVVSNAGIFTPSQNLDELSDENWQRSMDI 508

Query: 537 LGTGYFLVAREAFKQMKHQNRGGSMVFVGSKNSVYAGKNASAYSSVKALETHLARCIAAE 596
             T +  + + +   +K       +V V SKN    GK A+AYS  KA +T LAR  A E
Sbjct: 509 NLTSHQKLLKYSAPFLK-LGVEPCIVMVASKNFPAPGKGAAAYSVAKAGQTQLARIAALE 567

Query: 597 GGEFGIRVNSVLPDAVLQGSAIWGSSWREERAAAYGIEPDQLEEHYRKRTALLVNIYPED 656
            GEFG+RVN++ P AV   +AIW       RA AY +      E Y+    L   I   D
Sbjct: 568 LGEFGVRVNTLHPHAVFD-TAIWSDEVLANRAKAYKMS----VEEYKTNNVLKTEICSND 622

Query: 657 IAEAIAFFASSKAEKTTGCMITVDGG 682
           +AE +   A     KTTG  + +DGG
Sbjct: 623 VAELVCAMAGKPFAKTTGAQVAIDGG 648


Lambda     K      H
   0.317    0.134    0.396 

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: 957
Number of extensions: 43
Number of successful extensions: 7
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: 689
Length of database: 653
Length adjustment: 39
Effective length of query: 650
Effective length of database: 614
Effective search space:   399100
Effective search space used:   399100
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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