Alignments for a candidate for aldA in Chlorobaculum tepidum TLS

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldA in Chlorobaculum tepidum TLS

Align bifunctional L-rhamnulose 1-phosphate aldolase/lactaldehyde dehydrogenase (EC 4.1.2.19; EC 1.2.1.22) (characterized)
to candidate NP_662653.1 CT1774 short chain dehydrogenase

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



>NCBI__GCF_000006985.1:NP_662653.1
          Length = 694

 Score =  332 bits (852), Expect = 3e-95
 Identities = 219/708 (30%), Positives = 356/708 (50%), Gaps = 50/708 (7%)

Query: 11  AAQLPKGVEELVYRSNLIGSDRTVCNWGGGNTSMKTTEKDFRGREIEVMWVKGSGSDLAT 70
           AA  P  + ELVY S L+G D  +   GGGNTS+K    DF G  + V+++K SG +LA+
Sbjct: 8   AADTPAELVELVYASRLLGKDDRLVMHGGGNTSVKCELTDFIGNHVNVIFIKASGVNLAS 67

Query: 71  MKAHNFSGLKLDDIRPLIKR---DQMPDEEMVDYLS------------HCMID---SKHP 112
           + A +F+ +++D +R L K     Q   EE +   S              + D   S+  
Sbjct: 68  VDAGDFTPVRIDPLRKLQKMYESGQRHSEEDIRRFSTREFKNFLYLNLFTLTDHMVSRSL 127

Query: 113 RPSIETLLHAFLPYKHVDHTHPDAIISICCADNGKQIAEDIYGNRFVWVPYVRPGFTLSK 172
            PSIETLLHAFLP++++ HTH  A++++    +G+++  +  G+ +  VPY++PG  L+ 
Sbjct: 128 SPSIETLLHAFLPHRYILHTHSLALLTLSNQTDGERLCREALGDGYGQVPYIQPGLGLAN 187

Query: 173 MIAEGVANNPHAELVLMEKHGLVTWGETSETCYQKTISIIQEAEQYINDRINQHEVFGGK 232
           +  +    NP  E +++ KHGLVT+G++++  Y + I  +   E+ I            K
Sbjct: 188 LAHDAYEKNPSIEGLVLHKHGLVTFGDSAKEAYDRMIDGVNRIEERIASAAR-------K 240

Query: 233 RYQPLPEDKRKQILAGIMPVIRGAVSEEK--------KMILSYDDHDDVLEFVNSVQAPA 284
            +   P       +  + P++RGA S EK          +L +     +L+++      A
Sbjct: 241 VFASAPMPTAIASVEEVAPIVRGACSFEKTPGEKDYQSFVLEFRTSPALLDYLKIADLEA 300

Query: 285 LSQIGAACPDHLVHTKRVPLYIDWNPETQDVHKLADLIKSGVETFTSEYQAYFTRNQQDG 344
            S+ GA  PD ++ TK  PL     P+  D+      +++  + FT EY++YF R QQ  
Sbjct: 301 FSKKGAMTPDFIIRTKNHPLVAP-APDAADLEGFGKELRARAKRFTEEYRSYFERQQQAT 359

Query: 345 DQ---IFESAPRVILIPGIGMVNTGKSYAMSKVSGALYRRAIAVMKGATALGQFVSLHEN 401
                + +  PRV+L+PG+G+   G S A +K++  +   +   M  A ++G F S+ E 
Sbjct: 360 GMDVSMIDPMPRVVLVPGLGLFGLGLSAADAKLTADIAEHSAVAMLDAESIGCFESISEK 419

Query: 402 ESYHVEYWPLELYKLTLAPPEAEFSRKVALITGGAGGIGSAACRRFAAEGGHVIVADLNI 461
           E++ +EYW +E  K+  +    EF+ KVAL+TGGAG IG A  + F A+G  +++ D++ 
Sbjct: 420 EAFEIEYWDMEQAKVRKSHNGGEFAGKVALVTGGAGAIGLATAKAFKAKGAEIVIMDIDP 479

Query: 462 EGAQKIAGEINDAYGKGRAMAVKMDVTKEEDVQSAFERAALAYGGIDIVVNNAGLATSSP 521
              +K A E+    G G  + +  DVT    V+ AF+     +GG+DIVV+N G+A    
Sbjct: 480 AALEKAAAEL----GSG-TLTIPCDVTNAAAVREAFDTVCRTFGGLDIVVSNVGVAWQGR 534

Query: 522 FDETSLKEWNLNMNVLGTGYFLVAREAFKQMKHQNRGGSMVFVGSKNSVYAGKNASAYSS 581
             + S +    +  +    +  V++ A + M+ Q  GG +++  SK +V  G +   Y  
Sbjct: 535 IGDVSDELLRRSFELNFFSHQTVSQNAVRIMRRQGIGGVLLYNVSKQAVNPGPDFGPYGL 594

Query: 582 VKALETHLARCIAAEGGEFGIRVNSVLPDAVLQGSAIWGSSWREERAAAYGIEPDQLEEH 641
            KA    L R  A + G  GIR N V  D +  G  +      + R+AA G+     E  
Sbjct: 595 PKAATLFLLRQYALDHGRDGIRANGVNADRIRSG--LLTPEMIKARSAARGLS----ERD 648

Query: 642 YRKRTALLVNIYPEDIAEAIAFFASSKAEKTTGCMITVDGGVPAAFTR 689
           Y     L + +  ED+A+A    A     KTTG + TVDGG  AA  R
Sbjct: 649 YMAGNLLGLEVSAEDVADAFVHLALE--TKTTGSITTVDGGNIAAALR 694


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: 951
Number of extensions: 42
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: 689
Length of database: 694
Length adjustment: 39
Effective length of query: 650
Effective length of database: 655
Effective search space:   425750
Effective search space used:   425750
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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Protein sequences (fasta format)
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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