Alignments for a candidate for odc in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for odc in Methylobacterium nodulans ORS 2060

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate WP_015927042.1 MNOD_RS01410 Orn/Lys/Arg decarboxylase N-terminal domain-containing protein

Query= BRENDA::P21169
         (711 letters)



>NCBI__GCF_000022085.1:WP_015927042.1
          Length = 786

 Score =  577 bits (1486), Expect = e-168
 Identities = 306/650 (47%), Positives = 394/650 (60%), Gaps = 26/650 (4%)

Query: 88  LESAACQYEENLLPPFYDTLTQYVEMGNSTFACPGHQHGAFFKKHPAGRHFYDFFGENVF 147
           L S   QY E L  PF+  L  Y E GN  + CPGH  G F+ + P GR F +  GE +F
Sbjct: 129 LVSRVTQYAETLKTPFFGALVDYAEKGNQLWTCPGHNGGIFYNRSPIGRIFVEHLGEAIF 188

Query: 148 RADMCNADVKLGDLLIHEGSAKDAQKFAAKVFHADKTYFVLNGTSAANKVVTNALLTRGD 207
           R D+ N+ + LGDLL HEG A  AQK AA +F A+KTYFVLNGTSA+NK+V +AL+   D
Sbjct: 189 RDDLDNSVLDLGDLLTHEGPALKAQKEAAAIFGAEKTYFVLNGTSASNKIVLSALVAEDD 248

Query: 208 LVLFDRNNHKSNHHGALIQAGATPVYLEASRNPFGFIGGIDAHCFNEEYLRQQIRD---V 264
           LVLFDRNNHK+ HHGAL   G  P++LE  RN  G IG I    F+E  +R +IR    V
Sbjct: 249 LVLFDRNNHKAAHHGALFLGGGIPIFLETDRNAHGLIGPIYHEAFDEAAIRDKIRRNPLV 308

Query: 265 APEKA-DLPRPYRLAIIQLGTYDGTVYNARQVIDTVGHLCDYILFDSAWVGYEQFIPMMA 323
              +A    RP+R+A+I+  TYDGT+Y+AR+++  +GHLCDYILFD AW G+ +F P+ A
Sbjct: 309 RDRQAWRRQRPFRVAVIEQCTYDGTIYDAREILARIGHLCDYILFDEAWAGFMKFHPLYA 368

Query: 324 DSSPLLLE-LNENDPGIFVTQSVHKQQAGFSQTSQIHKKDNHIRGQARFCPHKRLNNAFM 382
               + L+ L  + PGI  TQS HKQ A FSQ SQIH KD HIRGQ+R   H+RLN +F+
Sbjct: 369 GRFAMGLDGLGPDSPGIIATQSTHKQLASFSQASQIHTKDGHIRGQSRRVEHRRLNESFL 428

Query: 383 LHASTSPFYPLFAALDVNAKIHEGESGRRLWAECVEIGIEARKAILARCK---------- 432
           +HASTSPFYPLFA+LDV A++ +G SG  LW + + +GIE RK + A  K          
Sbjct: 429 VHASTSPFYPLFASLDVGAQMMKGRSGMILWDDTIRLGIEWRKKVRAIRKEFEENEADPQ 488

Query: 433 ---LFRPFIPPVVDGK-----LWQDYPTSVLASDRRFFSFEPGAKWHGFEGYAADQYFVD 484
               F PF+P +V+G       W+  PT +LAS+ R++   PGA+WHGF   A      D
Sbjct: 489 RRWFFDPFVPDLVEGPDGTVLPWESLPTDLLASEPRYWELAPGARWHGFTKVAPGYAITD 548

Query: 485 PCKLLLTTPGIDAETGEYSDFGVPATILAHYLRENGIVPEKCDLNSILFLLTPAESHEKL 544
           P KL + TPG D ETGEY++ GVPA I+A YLREN IVPEK DLNS+LFLLTP     K 
Sbjct: 549 PNKLTVLTPGFDRETGEYAEHGVPAPIVAQYLRENRIVPEKNDLNSLLFLLTPGVESSKA 608

Query: 545 AQLVAMLAQFEQHIEDDSPLVEVLPSVYNKYPVRYRDYTLRQLCQEMHDLYVSFDVKDLQ 604
             L++ L  F++  +D+ PL E +P    + P RY+   LR LC E H  +       LQ
Sbjct: 609 GTLISGLVAFKRLHDDNVPLEEAMPDFVRRRPRRYQGVRLRDLCAEFHAFHREAGTSTLQ 668

Query: 605 KAMFRQQSFPSVVMNPQDAHSAYIRGDVELVRIRDAEGRIAAEGALPYPPGVLCVVPGEV 664
           +  F  +  P + M P+ A     R  V+ V I +A GRIA    L YPPG+  V+PGE 
Sbjct: 669 RKQFAPEHLPEMAMPPKAAAQMLTRNQVDFVPIAEAAGRIATTLMLVYPPGIGTVLPGER 728

Query: 665 WGGAVQ---RYFLALEEGVNLLPGFSPELQGVYSETDADGVKRLYGYVLK 711
                +    YF   E   NL PGF  E+QGVY + + DG  R Y YVL+
Sbjct: 729 LDERAKPMLDYFTMFETSANLFPGFEAEIQGVYRQVEPDGRIRFYTYVLR 778


Lambda     K      H
   0.322    0.138    0.420 

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: 1494
Number of extensions: 69
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: 711
Length of database: 786
Length adjustment: 40
Effective length of query: 671
Effective length of database: 746
Effective search space:   500566
Effective search space used:   500566
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 (21.9 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