GapMind for catabolism of small carbon sources

 

Alignments 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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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