Alignments for a candidate for adh in Marinicella litoralis KMM 3900

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Marinicella litoralis KMM 3900

Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate WP_099017976.1 CCS90_RS02790 aldehyde dehydrogenase family protein

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



>NCBI__GCF_002591915.1:WP_099017976.1
          Length = 787

 Score =  948 bits (2450), Expect = 0.0
 Identities = 470/796 (59%), Positives = 588/796 (73%), Gaps = 10/796 (1%)

Query: 1   MSVAEYFSSMDYGPAPEDDQPARQWLAQHEARFGHFIGGAWHAPASGAQFVSHAPASGER 60
           M++ +   +MDYG APE    A +WLAQH+ +  HFI G WH+  +   F S+ PASGER
Sbjct: 1   MNIKDILQTMDYGNAPESPDLALEWLAQHKNKMSHFINGDWHSGKN--HFASNNPASGER 58

Query: 61  LADIAQGDAADIDAALAAARAAQPGWLALGGKGRARHLYALARMVQRHSRLFAVLEALDN 120
           LA ++Q D   ++ A+ AA  A PGW AL G  R+ +LYA+AR++Q++SRLFAVLE LDN
Sbjct: 59  LAQVSQADKNTVNQAVKAAEKALPGWQALSGHARSEYLYAIARLIQKNSRLFAVLETLDN 118

Query: 121 GKPIRETRDLDVPLVARHFLHHAGWAQLQDSEFADHAPLGVIGQIVPWNFPLLMLAWKIA 180
           GKPIRE+RD+DVPL  RHF HHAGWAQL D+EF DH  +GV+GQI+PWNFPLLMLAWKIA
Sbjct: 119 GKPIRESRDIDVPLAIRHFYHHAGWAQLLDTEFPDHEAIGVVGQIIPWNFPLLMLAWKIA 178

Query: 181 PAIATGNCVVLKPAEYTPLTALLFAELAHQAGLPAGVLNVVTGDGSTGAALVEHPQVDKI 240
           PA+ATGN +V+KPAE+T LTALLFAE+  QAGLP GVLNVVTGDGSTG  +VEHP + KI
Sbjct: 179 PALATGNTIVIKPAEFTSLTALLFAEICQQAGLPKGVLNVVTGDGSTGQHIVEHPDIKKI 238

Query: 241 AFTGSTEVGKLIRSVTAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVC 300
           AFTGST VG+ IR  TAGSGK L+LELGGKS FIV  DADLD AVEGVVDAIWFNQGQVC
Sbjct: 239 AFTGSTAVGRWIRQATAGSGKKLSLELGGKSAFIVCADADLDAAVEGVVDAIWFNQGQVC 298

Query: 301 CAGSRLLVQEGIEARFIAKLKRRMETLRVGPSLDKSIDMGAIVDPVQLERIHSLVETGRR 360
           CAGSRLLVQE +  RF  KL  RM  LR+G  LDKSIDMGAI+DP Q ++I SLV+ G  
Sbjct: 299 CAGSRLLVQEAVAERFHKKLISRMHKLRIGDPLDKSIDMGAIIDPRQQQKIASLVQAGVD 358

Query: 361 EGCAIWQAADTPLPANGCFYPPTLVTNVAPASTLAQEEIFGPVLVTMSFRTPDEAIALAN 420
            G  + Q+    LP++GCFYPPTL+T+V+P+  + Q+EIFGPVLV+M+FRTP EA+ALAN
Sbjct: 359 AGACLNQST-AELPSSGCFYPPTLLTDVSPSDQVVQDEIFGPVLVSMTFRTPSEAVALAN 417

Query: 421 NSRYGLAASVWSETIGRALDVAPRLAAGVVWVNATNLFDAAVGFGGYRESGYGREGGREG 480
           NSRYGLAAS+WSE I  A+ +AP + AG+VW+N TN+ DAA GFGG +ESG+GREGG+EG
Sbjct: 418 NSRYGLAASIWSENINMAMHLAPLVQAGIVWINCTNMMDAAAGFGGVKESGFGREGGKEG 477

Query: 481 IHEYLKPRAWLNLPKRQPVSAATNASDDRQVSNLALVDRTAKLFIGGKQVRPDSGYSLPV 540
           ++EYL  +  +N   ++    A N    + +  +  +D+T K++IGGKQVRPD GYS  +
Sbjct: 478 LYEYLTLK--INTKTQKDKDKAANKQAAKSIEPVQGMDKTPKMYIGGKQVRPDGGYSYAI 535

Query: 541 HAPDGTRVGEVGEGNRKDIRNAVQAARAAQKWSQASTHNRAQVLFYLAENLAVRADEFAH 600
           H   G  +   G GNRKD+RNAV+AA  +  WS  + + R QV++++AENL+ R  EFA 
Sbjct: 536 HNSKGQIITHAGLGNRKDVRNAVEAAATSHSWSHMNAYQRQQVMYFMAENLSYRKAEFAT 595

Query: 601 QLTVRNGATDAAAHAEVEASVTRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGVIGIA 660
           +L    G +   A  EVE+S+ RL  YAAW DKFDG +H+ P+RGV +AMHEP+GVI I 
Sbjct: 596 RLE-SFGHSKKQAETEVESSIQRLSYYAAWCDKFDGQIHSVPMRGVVMAMHEPIGVIAIQ 654

Query: 661 CPDEAPLLAFVSLAAPALAMGNRVVVLPGEACPLAVTDFYQVVETSDVPGGVVNIVTGKR 720
           CPDEAPLL+F+SL APA+AMGNRVV+   EA PL+  DFYQV+ TSDVP G VNI++G R
Sbjct: 655 CPDEAPLLSFISLLAPAIAMGNRVVMTASEAFPLSALDFYQVLNTSDVPAGTVNIISGNR 714

Query: 721 EALLPALARHDDVDAVWCFGSAADATLIERESVGNLKRTFTDYGRQFDWFD-RASEGLPF 779
             L   LA H +VDA+W FGS  DA  +E ES  NLKR++T    + DW +    +G  F
Sbjct: 715 LELTKPLAGHMNVDAIWAFGS--DAQWVEHESATNLKRSWTQNSHR-DWLNINQGQGQEF 771

Query: 780 LRQAVQVKNIWIPYGD 795
           LR+A QVKNIW PYG+
Sbjct: 772 LRRATQVKNIWTPYGE 787


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: 1662
Number of extensions: 70
Number of successful extensions: 9
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: 787
Length adjustment: 41
Effective length of query: 754
Effective length of database: 746
Effective search space:   562484
Effective search space used:   562484
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 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

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
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