Aligments for a candidate for aldA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Aligments for a candidate for aldA in Dinoroseobacter shibae DFL-12

Align rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate 3609047 Dshi_2436 rhamnulose-1-phosphate aldolase/alcohol dehydrogenase (RefSeq)

Query= reanno::Dino:3609047
         (700 letters)



>FitnessBrowser__Dino:3609047
          Length = 700

 Score = 1385 bits (3586), Expect = 0.0
 Identities = 700/700 (100%), Positives = 700/700 (100%)

Query: 1   MLKSLETQLLESRWDDEVAKGMSESELLLYRSNILGADKRVTNYGGGNTSAKVMEADPLT 60
           MLKSLETQLLESRWDDEVAKGMSESELLLYRSNILGADKRVTNYGGGNTSAKVMEADPLT
Sbjct: 1   MLKSLETQLLESRWDDEVAKGMSESELLLYRSNILGADKRVTNYGGGNTSAKVMEADPLT 60

Query: 61  GAQVEVLWVKGSGGDIGSIKMDGFATLYMDKLRALKGLYRGVAFEDEMVSYLPHCTFRLN 120
           GAQVEVLWVKGSGGDIGSIKMDGFATLYMDKLRALKGLYRGVAFEDEMVSYLPHCTFRLN
Sbjct: 61  GAQVEVLWVKGSGGDIGSIKMDGFATLYMDKLRALKGLYRGVAFEDEMVSYLPHCTFRLN 120

Query: 121 PRAASIDTPLHAYVPRKHVDHVHADAIIAIAASDNSKELTQEIFGNRIGWLPWKRPGFEL 180
           PRAASIDTPLHAYVPRKHVDHVHADAIIAIAASDNSKELTQEIFGNRIGWLPWKRPGFEL
Sbjct: 121 PRAASIDTPLHAYVPRKHVDHVHADAIIAIAASDNSKELTQEIFGNRIGWLPWKRPGFEL 180

Query: 181 GLWLEKFCRENPEADGVVLESHGLFTWADTAKECYDQTIDVINVATRWLAERSAGVPAFG 240
           GLWLEKFCRENPEADGVVLESHGLFTWADTAKECYDQTIDVINVATRWLAERSAGVPAFG
Sbjct: 181 GLWLEKFCRENPEADGVVLESHGLFTWADTAKECYDQTIDVINVATRWLAERSAGVPAFG 240

Query: 241 GAIHESLPAAARREVAARLMPAIRGFVSDNQHMVGHFNDSDAVLEFVNARDMEALAALGT 300
           GAIHESLPAAARREVAARLMPAIRGFVSDNQHMVGHFNDSDAVLEFVNARDMEALAALGT
Sbjct: 241 GAIHESLPAAARREVAARLMPAIRGFVSDNQHMVGHFNDSDAVLEFVNARDMEALAALGT 300

Query: 301 SCPDHFLRTKIRPLVVPFDPAQNNILAVLSELPDQVAAYREAYAAYYARCKHDDSPALRD 360
           SCPDHFLRTKIRPLVVPFDPAQNNILAVLSELPDQVAAYREAYAAYYARCKHDDSPALRD
Sbjct: 301 SCPDHFLRTKIRPLVVPFDPAQNNILAVLSELPDQVAAYREAYAAYYARCKHDDSPALRD 360

Query: 361 PNAVVYLVPGVGMITFAKDKATARISGEFYVNAINVMRGASAVSTYQGLPEQEAFDIEYW 420
           PNAVVYLVPGVGMITFAKDKATARISGEFYVNAINVMRGASAVSTYQGLPEQEAFDIEYW
Sbjct: 361 PNAVVYLVPGVGMITFAKDKATARISGEFYVNAINVMRGASAVSTYQGLPEQEAFDIEYW 420

Query: 421 LLEEAKLQRMPKPKSLAGRVALVTGGAGGIGAATAERFLAEGACVVLADINEDSLASTQE 480
           LLEEAKLQRMPKPKSLAGRVALVTGGAGGIGAATAERFLAEGACVVLADINEDSLASTQE
Sbjct: 421 LLEEAKLQRMPKPKSLAGRVALVTGGAGGIGAATAERFLAEGACVVLADINEDSLASTQE 480

Query: 481 RLSERFGADVVRSVVMNVTREEAVAAAFAEASVEFGGVDILVSNAGIASSAPIEETSLAL 540
           RLSERFGADVVRSVVMNVTREEAVAAAFAEASVEFGGVDILVSNAGIASSAPIEETSLAL
Sbjct: 481 RLSERFGADVVRSVVMNVTREEAVAAAFAEASVEFGGVDILVSNAGIASSAPIEETSLAL 540

Query: 541 WNKNMDILSTGYFLVSRAAFKLMRVQDMGGAVVFVASKNGLAASPNAAAYCTAKASEIHL 600
           WNKNMDILSTGYFLVSRAAFKLMRVQDMGGAVVFVASKNGLAASPNAAAYCTAKASEIHL
Sbjct: 541 WNKNMDILSTGYFLVSRAAFKLMRVQDMGGAVVFVASKNGLAASPNAAAYCTAKASEIHL 600

Query: 601 ARCLALEGAEAGIRVNVVNPDAVLRGSKIWEGDWLEQRAGTYGTDKDGLEEMYRQRSLLK 660
           ARCLALEGAEAGIRVNVVNPDAVLRGSKIWEGDWLEQRAGTYGTDKDGLEEMYRQRSLLK
Sbjct: 601 ARCLALEGAEAGIRVNVVNPDAVLRGSKIWEGDWLEQRAGTYGTDKDGLEEMYRQRSLLK 660

Query: 661 RSVLPEDIAEACYFFAADASSKSTGNIINVDAGNVQAFTR 700
           RSVLPEDIAEACYFFAADASSKSTGNIINVDAGNVQAFTR
Sbjct: 661 RSVLPEDIAEACYFFAADASSKSTGNIINVDAGNVQAFTR 700


Lambda     K      H
   0.318    0.133    0.391 

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: 1471
Number of extensions: 37
Number of successful extensions: 1
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: 700
Length of database: 700
Length adjustment: 39
Effective length of query: 661
Effective length of database: 661
Effective search space:   436921
Effective search space used:   436921
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 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, or view the source code.

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