GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Trichormus variabilis ATCC 29413

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein

Query= BRENDA::P25553
         (479 letters)



>NCBI__GCF_000204075.1:WP_011318370.1
          Length = 498

 Score =  277 bits (709), Expect = 5e-79
 Identities = 158/443 (35%), Positives = 250/443 (56%), Gaps = 6/443 (1%)

Query: 1   MSVPVQHPMYIDGQFVTWRGDAWIDVVNPATEA-VISRIPDGQAEDARKAIDAAERAQPE 59
           M  P+    YI+GQ++    +  ++  NPA ++ +++  P  QA+D  +A+ AA +A   
Sbjct: 1   MKTPLNCQNYINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYGS 60

Query: 60  WEALPAIERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWA 119
           W  +PA  RA ++ ++   + +   E++ LI  E GK    A  +V    D   Y A   
Sbjct: 61  WRKVPAPARAEYIFRVGELLLQHKEELAQLISREMGKPITEARGDVQEGVDCAFYSAGEG 120

Query: 120 RRYEGEIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSE 179
           RR  G+   S+ P +  +  +  +GV   I PWNFP  +   K  PAL+ GNT+++KP+E
Sbjct: 121 RRLFGQTTPSEMPNKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAE 180

Query: 180 FTPNNAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMA 239
            TP  A    +I    GLP GV NLV G GE  G+ L  +P + +VS TGS + G  +  
Sbjct: 181 DTPACATKLIEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVGE 240

Query: 240 TAAKNITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYD 299
           T  +   +VCLE+GGK   +VM+DADLELA+   +      +GQ C    R+ + + I +
Sbjct: 241 TCGRTHKRVCLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIKE 300

Query: 300 QFVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAV- 358
           +F   L E    ++ G   E  +  +GP+IN   L+RV + +  A EEGA++  GG+ V 
Sbjct: 301 KFTTMLRERTSQLRLGAGTE-PETDIGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVT 359

Query: 359 EG---KGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSI 415
           EG   +GY++ PT+L +V  +M +  EE FGPV+ ++   T E+AI++ ND+ YGL+SS+
Sbjct: 360 EGQLKQGYFFQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSV 419

Query: 416 YTQNLNVAMKAIKGLKFGETYIN 438
           YT+++N A  A++ ++ G TYIN
Sbjct: 420 YTRDINRAFVAMRDIEVGITYIN 442


Lambda     K      H
   0.318    0.135    0.392 

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: 587
Number of extensions: 23
Number of successful extensions: 4
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: 479
Length of database: 498
Length adjustment: 34
Effective length of query: 445
Effective length of database: 464
Effective search space:   206480
Effective search space used:   206480
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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:

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:

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:

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:

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