Alignments for a candidate for adh in Rhizobium leguminosarum bv. trifolii WSM1325

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Rhizobium leguminosarum bv. trifolii WSM1325

Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate WP_012757758.1 RLEG_RS11275 aldehyde dehydrogenase family protein

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



>NCBI__GCF_000023185.1:WP_012757758.1
          Length = 795

 Score = 1084 bits (2804), Expect = 0.0
 Identities = 541/797 (67%), Positives = 637/797 (79%), Gaps = 3/797 (0%)

Query: 1   MSVAEYFSSMEYGPAPEDDQPARAWLAQHEDGFGHFIGGAWHAPAAGERFASNAPATGEQ 60
           M+VA+YF  M YGPAPE D  AR WLA+H  GFGHFI GA+   A+ + F +  PATG+ 
Sbjct: 1   MTVAKYFDEMSYGPAPESDIEARDWLARHASGFGHFINGAFVPSASVKNFDTFEPATGKV 60

Query: 61  LAQVAQGDAADIDAAVAAARAAQPGWLALGGAGRARHLYALARMVQRHSRLFAVLEALDN 120
           LA++A G AAD+D AVAAAR AQ  W  L G  RARHLYALARM+QRH+RL AV+EA+DN
Sbjct: 61  LAKLANGGAADVDNAVAAARKAQASWARLPGHARARHLYALARMIQRHARLIAVVEAIDN 120

Query: 121 GKPIRETRDIDVPLVARHFLHHAGWAQLQESEFADYAPLGVVGQIVPWNFPLLMLAWKIA 180
           GKPIRETRD+DVPL ARHF HHAGWAQ+Q++EFAD+ P+GVVGQI+PWNFP LMLAWK+A
Sbjct: 121 GKPIRETRDLDVPLAARHFYHHAGWAQIQDTEFADHVPVGVVGQIIPWNFPFLMLAWKVA 180

Query: 181 PAIATGNCVVLKPAEYTPLTALLFAELAHRAGLPAGVLNVVTGDGRTGAALVEHPQVDKI 240
           PA+A GN V+LKPAE+T LTALLFAELA  AGLP GVLN+VTG+G TGA LV H  +DKI
Sbjct: 181 PALALGNTVILKPAEFTSLTALLFAELASAAGLPPGVLNIVTGEGETGALLVGHADIDKI 240

Query: 241 AFTGSTEVGRLIRSATAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVC 300
           AFTGSTEVGR+IR  TAGSGKSLTLELGGKSPF+VFDDAD+DGAVEGVVDAIWFNQGQVC
Sbjct: 241 AFTGSTEVGRVIRERTAGSGKSLTLELGGKSPFVVFDDADIDGAVEGVVDAIWFNQGQVC 300

Query: 301 CAGSRLLVQEGIEARFIAKLKRRMETLRVGTSLDKSIDLGAIVDPVQLERIQSLVETGRR 360
           CAGSRLLVQEGI   F  +LKRRMETLRVG  LDK ID+GAI+ PVQL RI++LV+ G  
Sbjct: 301 CAGSRLLVQEGIADLFHERLKRRMETLRVGQPLDKCIDMGAIIAPVQLTRIEALVKKGVS 360

Query: 361 EGCSVWQSPDTTIPSGGCFFPPTLVTGVAPASTLAQEEIFGPVLVTMSFRTPDEAIALAN 420
           EG ++ Q+    +P GG F+PPTL++GV P S +A EEIFGPV V+M+FRTP+EAI LAN
Sbjct: 361 EGATLHQA-KIDLPKGGSFYPPTLLSGVQPTSIVATEEIFGPVAVSMTFRTPEEAIQLAN 419

Query: 421 NSRYGLAASVWSETIGRALDVAPRLASGVVWINATNLFDAAVGFGGYRESGYGREGGREG 480
           ++RYGLAASVWSETIG AL+VA +LA+GVVW+NATNLFDAAVGFGG RESG+GREGGREG
Sbjct: 420 HTRYGLAASVWSETIGLALNVAAKLAAGVVWVNATNLFDAAVGFGGKRESGFGREGGREG 479

Query: 481 IYEYLKPRAWLKLAERRAAQDVVRDAAALDPLSNVTSIDRTAKLFIGGKQARPDSGYSLP 540
            YEYLKP+AW+   + RAA   +  A  +     + SIDRTAKLFIGGKQARPD  YS  
Sbjct: 480 CYEYLKPKAWVG-RKARAAMPALSQAKPVAGDFALPSIDRTAKLFIGGKQARPDGNYSRV 538

Query: 541 VLAPDGTPVGEVAAGNRKDIRNAVEAARAAQKWSQASTHNRAQVLFYLAENLAVRADEFV 600
           + +P G  +GEV   NRKDIRNAV AA+AA  WS A+THNRAQ+L+Y+AENL+ RADEF 
Sbjct: 539 IASPKGKAIGEVGESNRKDIRNAVVAAQAASAWSNATTHNRAQILYYIAENLSGRADEFA 598

Query: 601 RQLVVRNGATEAAARAEVDASVQRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGVIGI 660
            ++    GA+ A A AEVDA++ RLFTYAAWADK++G +H PPLRGVALAM E +GV+G+
Sbjct: 599 SRITAMTGASAANANAEVDAAISRLFTYAAWADKYEGGIHQPPLRGVALAMPEAIGVVGV 658

Query: 661 ACPDEAPLLGFVSLAAPALAMGNRVVVLPSEASPLTVTDFYQVAETSDVPGGVLNIVTGE 720
            CP EAPLLGF+SL AP +A GNRVV +PSEA PL+ TDFY V ETSDVP GV+NIVTG 
Sbjct: 659 ICPPEAPLLGFISLIAPLIATGNRVVAVPSEAFPLSATDFYSVLETSDVPAGVVNIVTGS 718

Query: 721 RGALLPALVKHDDVDAVWCFGSAADSTLVERESVGNLKRTFVDYGRQFDWFDR-ASEGRP 779
              L   L  H+DVDA+W FGSA  ST VE+ S GNLKRTFVD G+  DW D+ A+EG  
Sbjct: 719 AIELAKILAAHNDVDALWAFGSAELSTTVEKLSSGNLKRTFVDNGKATDWMDKAAAEGAL 778

Query: 780 FLRQAVQVKNIWIPYGD 796
           +LR+AV VKNIWIPYG+
Sbjct: 779 YLRRAVDVKNIWIPYGE 795


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: 1794
Number of extensions: 63
Number of successful extensions: 8
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: 795
Length adjustment: 41
Effective length of query: 755
Effective length of database: 754
Effective search space:   569270
Effective search space used:   569270
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 Apr 09 2024. 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