Alignments for a candidate for adh in Marivita geojedonensis DPG-138

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Marivita geojedonensis DPG-138

Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate WP_085635023.1 MGEO_RS02095 aldehyde dehydrogenase family protein

Query= reanno::BFirm:BPHYT_RS25810
         (796 letters)



>NCBI__GCF_002115805.1:WP_085635023.1
          Length = 782

 Score =  959 bits (2479), Expect = 0.0
 Identities = 493/800 (61%), Positives = 579/800 (72%), Gaps = 24/800 (3%)

Query: 1   MSVAEYFSSMEYGPAPEDDQPARAWLAQHEDGFGHFIGGAWHAPAAGERFASNAPATGEQ 60
           M+V E F SM+YG APE    A AWL    D FGHFI GA      G+ F S  PA GE 
Sbjct: 1   MTVQEIFESMDYGTAPESAADALAWLVDQGDQFGHFINGAM--TDRGQVFESLNPANGEV 58

Query: 61  LAQVAQGDAADIDAAVAAARAAQPGWLALGGAGRARHLYALARMVQRHSRLFAVLEALDN 120
           LA + QG  AD+DAAVAAAR AQ GW  LGG GRAR+LYALAR++Q+H+RLFAVLE LDN
Sbjct: 59  LAHLTQGTQADVDAAVAAARKAQKGWAKLGGTGRARYLYALARLMQKHARLFAVLETLDN 118

Query: 121 GKPIRETRDIDVPLVARHFLHHAGWAQLQESEFADYAPLGVVGQIVPWNFPLLMLAWKIA 180
           GKPIRE+RDIDVPL  RHF +HAG AQL ESEFA     GV GQ++PWNFPLLMLAWK+A
Sbjct: 119 GKPIRESRDIDVPLAQRHFYYHAGQAQLFESEFAGREAHGVCGQVIPWNFPLLMLAWKVA 178

Query: 181 PAIATGNCVVLKPAEYTPLTALLFAELAHRAGLPAGVLNVVTGDGRTGAALVEHPQVDKI 240
           PA+A GN VVLKPAEYT LTALLFA++  +AGLP GV+N+VTGDG  G  +V HP VDK+
Sbjct: 179 PALAAGNTVVLKPAEYTSLTALLFADICRQAGLPKGVVNIVTGDGAVGEMIVTHPDVDKV 238

Query: 241 AFTGSTEVGRLIRSATAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVC 300
           AFTGST VGR IR ATAGSGK+LTLELGGKSP+IVF+DADLD AVEG+VDAIW NQGQVC
Sbjct: 239 AFTGSTAVGRRIREATAGSGKALTLELGGKSPYIVFEDADLDSAVEGLVDAIWLNQGQVC 298

Query: 301 CAGSRLLVQEGIEARFIAKLKRRMETLRVGTSLDKSIDLGAIVDPVQLERIQSLVETGR- 359
           CAGSRLLVQEG+  RF AKLK RM+ LRVG+ LDKSID+GAIVDP QLE I  LV++   
Sbjct: 299 CAGSRLLVQEGVADRFYAKLKARMDKLRVGSPLDKSIDVGAIVDPRQLETITRLVDSNTV 358

Query: 360 ----REGCSVWQSPDTTIPSGGCFFPPTLVTGVAPASTLAQEEIFGPVLVTMSFRTPDEA 415
               R  C         +P  GCF+PPTL+TG+  A  L QEEIFGPVLV  +FRTP EA
Sbjct: 359 GETYRTNCE--------MPQNGCFYPPTLITGLNTADPLMQEEIFGPVLVGTTFRTPSEA 410

Query: 416 IALANNSRYGLAASVWSETIGRALDVAPRLASGVVWINATNLFDAAVGFGGYRESGYGRE 475
           + LANN+RYGLAA++WSE I  ALD+AP+LA+GVVW+N TN+FDAA  FGG RESG+GRE
Sbjct: 411 VDLANNTRYGLAATLWSENINVALDIAPKLAAGVVWVNGTNMFDAAAPFGGVRESGFGRE 470

Query: 476 GGREGIYEYLKPRAWLKLAERRAAQDVVRDAAALDPLSNVTSIDRTAKLFIGGKQARPDS 535
           GG EG+  Y KP    K   +        +  +  P +   ++DRTAKL++GGKQARPD 
Sbjct: 471 GGPEGMIAYTKPAGSGKAMSK-------IEGYSSGPDAEPQAVDRTAKLYVGGKQARPDG 523

Query: 536 GYSLPVLAPDGTPVGEVAAGNRKDIRNAVEAARAAQKWSQASTHNRAQVLFYLAENLAVR 595
           GY+  V    G  +G+    NRKD+RNAVEAAR A  W+  + H RAQ+L+Y+AENLA R
Sbjct: 524 GYAYEVYTKAGKLIGQAPLANRKDVRNAVEAARGAAGWAGTTAHLRAQILYYIAENLAAR 583

Query: 596 ADEFVRQLVVRNGATEAAARAEVDASVQRLFTYAAWADKFDGAVHTPPLRGVALAMHEPL 655
            DEF  +L    GA   A   EVD +V RLFTYAAWADKFDG V   PLRGVALAM EP 
Sbjct: 584 KDEFAARLNQMTGAKTGA--KEVDVAVNRLFTYAAWADKFDGRVAQVPLRGVALAMREPC 641

Query: 656 GVIGIACPDEAPLLGFVSLAAPALAMGNRVVVLPSEASPLTVTDFYQVAETSDVPGGVLN 715
           GVIG  CPD+ PLLG VS+ APA+AMGNRVV++ SE  PL  TDFYQV +TSDVPGGV+N
Sbjct: 642 GVIGAFCPDDHPLLGLVSVMAPAIAMGNRVVLVASEPFPLAATDFYQVLDTSDVPGGVVN 701

Query: 716 IVTGERGALLPALVKHDDVDAVWCFGSAADSTLVERESVGNLKRTFVDYGRQFDWFDRAS 775
           I+TG    L P L +H DV+AVW F S   S ++ER +  NLKRT+V+YGR  DW     
Sbjct: 702 ILTGRHAELAPTLAQHMDVEAVWSFSSTDLSAVIERGAALNLKRTWVNYGRGRDWMGSDG 761

Query: 776 EGRPFLRQAVQVKNIWIPYG 795
           EGR FL  A + K +W+PYG
Sbjct: 762 EGRVFLDAATETKTVWVPYG 781


Lambda     K      H
   0.319    0.135    0.408 

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: 1703
Number of extensions: 73
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: 796
Length of database: 782
Length adjustment: 41
Effective length of query: 755
Effective length of database: 741
Effective search space:   559455
Effective search space used:   559455
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.

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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 2024 update 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