Aligments for a candidate for adh in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments for a candidate for adh in Herbaspirillum seropedicae SmR1

Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate HSERO_RS05115 HSERO_RS05115 aldehyde dehydrogenase

Query= reanno::Burk376:H281DRAFT_01117
         (795 letters)



>FitnessBrowser__HerbieS:HSERO_RS05115
          Length = 793

 Score = 1072 bits (2772), Expect = 0.0
 Identities = 538/797 (67%), Positives = 621/797 (77%), Gaps = 6/797 (0%)

Query: 1   MSVAEYFSSMDYGPAPEDDQPARQWLAQHEARFGHFIGGAWHAPASGAQFVSHAPASGER 60
           MSV+ YF +MDYGPAPE D+ AR WLA HEA FGHFI G +  P +    +   PASG+ 
Sbjct: 1   MSVSTYFDTMDYGPAPESDKDARAWLASHEASFGHFIAGRFTQPKADLDDID--PASGKL 58

Query: 61  LADIAQGDAADIDAALAAARAAQPGWLALGGKGRARHLYALARMVQRHSRLFAVLEALDN 120
           LA ++QG AAD+DAA+ AA+AA PGW ALGG GRARHLYALAR VQRH+RL AVLE LDN
Sbjct: 59  LAHLSQGSAADVDAAVQAAQAALPGWQALGGHGRARHLYALARTVQRHARLLAVLETLDN 118

Query: 121 GKPIRETRDLDVPLVARHFLHHAGWAQLQDSEFADHAPLGVIGQIVPWNFPLLMLAWKIA 180
           GKP+RE+RD+DVPLVARHF H+AGWAQLQ+SEF DH P+GV+GQIVPWNFPLLMLAWKIA
Sbjct: 119 GKPLRESRDVDVPLVARHFYHYAGWAQLQESEFPDHVPVGVVGQIVPWNFPLLMLAWKIA 178

Query: 181 PAIATGNCVVLKPAEYTPLTALLFAELAHQAGLPAGVLNVVTGDGSTGAALVEHPQVDKI 240
           PA+A GN VVLKPAE T LTALLFAELA QAGLPAGVLN+VTGDG+TGAA+V HP + KI
Sbjct: 179 PALALGNTVVLKPAENTSLTALLFAELAQQAGLPAGVLNIVTGDGATGAAVVAHPGIQKI 238

Query: 241 AFTGSTEVGKLIRSVTAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVC 300
           AFTGSTEVG+LIR  TAGSGKSLTLELGGKSPFIVF+DAD+D A+EGVVDAIWFNQGQVC
Sbjct: 239 AFTGSTEVGRLIREQTAGSGKSLTLELGGKSPFIVFEDADIDAAIEGVVDAIWFNQGQVC 298

Query: 301 CAGSRLLVQEGIEARFIAKLKRRMETLRVGPSLDKSIDMGAIVDPVQLERIHSLVETGRR 360
           CAGSRLLVQEGI   FIA+LK RM+ L+VG  LDK  DMGA++ PVQLER+ SLVE G R
Sbjct: 299 CAGSRLLVQEGIHDLFIARLKTRMQKLKVGAPLDKCSDMGALISPVQLERVRSLVEQGVR 358

Query: 361 EGCAIWQAA-DTPLPANGCFYPPTLVTNVAPASTLAQEEIFGPVLVTMSFRTPDEAIALA 419
           EG    Q   DTP    GCFYPPTL+T V PA+T+A EEIFGPVLV MSFRTPDEA+ LA
Sbjct: 359 EGAQCHQVVLDTP--PGGCFYPPTLLTGVHPAATVASEEIFGPVLVAMSFRTPDEAVQLA 416

Query: 420 NNSRYGLAASVWSETIGRALDVAPRLAAGVVWVNATNLFDAAVGFGGYRESGYGREGGRE 479
           NNSRYGLAAS+WSETIG AL VAP+L AGVVW+N+TN FDAAVGFGG RESGYGREGGRE
Sbjct: 417 NNSRYGLAASIWSETIGLALGVAPQLKAGVVWINSTNQFDAAVGFGGVRESGYGREGGRE 476

Query: 480 GIHEYLKPRAWLNLPKRQPVSAATNASDDRQVSNLALVDRTAKLFIGGKQVRPDSGYSLP 539
           G +EYLKPR       RQP +     +D         +DRTAKL+IGGKQVRPD   S+ 
Sbjct: 477 GCYEYLKPRRQQAGSLRQPSARRAIRADADSPLQGGAIDRTAKLYIGGKQVRPDGEVSMA 536

Query: 540 VHAPDGTRVGEVGEGNRKDIRNAVQAARAAQKWSQASTHNRAQVLFYLAENLAVRADEFA 599
            H+  G R+ +VG GNRKDIRNAV AA  A  W+ AS H RAQ L+Y+AENL+ R +EFA
Sbjct: 537 CHSTQGERLEDVGLGNRKDIRNAVAAAVKAGGWTSASPHRRAQGLYYIAENLSARTEEFA 596

Query: 600 HQLTVRNGATDAAAHAEVEASVTRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGVIGI 659
            ++    G T   A AEV+AS+ RLFTY AWADKF+GAVH PP+RGVALAM E +GV+G+
Sbjct: 597 RRIASTTGVTADEARAEVDASIKRLFTYGAWADKFEGAVHQPPMRGVALAMPEAIGVVGV 656

Query: 660 ACPDEAPLLAFVSLAAPALAMGNRVVVLPGEACPLAVTDFYQVVETSDVPGGVVNIVTGK 719
            CP+E PLLA +SL AP +AMGNRVVV+P E  PL  TD YQV++TSD+P GV+NIVTGK
Sbjct: 657 VCPEEKPLLALISLVAPLIAMGNRVVVVPSEQAPLVATDLYQVLDTSDLPAGVINIVTGK 716

Query: 720 REALLPALARHDDVDAVWCFGSAADATLIERESVGNLKRTFTDYGRQFDWFDRA-SEGLP 778
              LLP LA HD+V+A+W  G A  +   ER S GNLKR F D+G   DW D A  EG  
Sbjct: 717 SAELLPVLAEHDEVEALWVRGPAEFSATAERLSTGNLKRCFVDHGYVTDWHDAAQGEGAQ 776

Query: 779 FLRQAVQVKNIWIPYGD 795
           +LRQA  +KN+WIPYG+
Sbjct: 777 YLRQATHIKNVWIPYGE 793


Lambda     K      H
   0.320    0.135    0.411 

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: 1850
Number of extensions: 65
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: 795
Length of database: 793
Length adjustment: 41
Effective length of query: 754
Effective length of database: 752
Effective search space:   567008
Effective search space used:   567008
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 17 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, 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