GapMind for catabolism of small carbon sources

 

Alignments for a candidate for odc in Methanospirillum lacunae Ki8-1

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate WP_109967963.1 DK846_RS05625 arginine decarboxylase

Query= BRENDA::P21169
         (711 letters)



>NCBI__GCF_003173355.1:WP_109967963.1
          Length = 767

 Score =  390 bits (1002), Expect = e-112
 Identities = 246/687 (35%), Positives = 356/687 (51%), Gaps = 46/687 (6%)

Query: 42  DSRSGILALLKRTGFHLPVFLYSEHAVELPAGVTAVINGNEQQWL------------ELE 89
           +S + I+  ++R    LP+FL +E A + P+G+T  I     +++             + 
Sbjct: 77  ESTTKIIHEIRRRNDELPIFLLAEPASQAPSGLTVEIIKEINEYVYAMDDTPDFLAGRIT 136

Query: 90  SAACQYEENLLPPFYDTLTQYVEMGNSTFACPGHQHGAFFKKHPAGRHFYDFFGENVFRA 149
           +AA +Y E +L PF+  L ++      ++  PGH  G  F+K P GR F+ FFGE +FR+
Sbjct: 137 AAARRYREQMLSPFFSELIKFSRDFEYSWHTPGHAGGTAFRKTPVGRAFHTFFGEQLFRS 196

Query: 150 DMCNADVKLGDLLIHEGSAKDAQKFAAKVFHADKTYFVLNGTSAANKVVTNALLTRGDLV 209
           D+  +  +LG LL H G    A+K+AAKVF ADKTYFV NGTS ANK+V    +T GD+V
Sbjct: 197 DLSISVDELGSLLDHSGPIGKAEKYAAKVFGADKTYFVTNGTSTANKIVFFGAVTEGDVV 256

Query: 210 LFDRNNHKSNHHGALIQAGATPVYLEASRNPFGFIGGIDAHCFNEEYLRQQIRDVAPEK- 268
           L DRN HKS  H AL    + PVYL  SRN +G IG I       + + ++++     K 
Sbjct: 257 LVDRNCHKSAEH-ALTMTHSVPVYLIPSRNRYGIIGPIHPDQLTPDAISKKVQACPFTKY 315

Query: 269 ADLPRPYRLAIIQLGTYDGTVYNARQVIDTVGHLCDYILFDSAWVGYEQFIPMMADSSPL 328
           AD   P   AII   TYDG  Y+A +V   +G   D I FD AW GY +F P+  D   +
Sbjct: 316 ADSDHPVH-AIITNSTYDGLCYHAARVEHLLGQTVDRIHFDEAWYGYARFNPLYRDRFAM 374

Query: 329 LLELNE-NDPGIFVTQSVHKQQAGFSQTSQIHKKDNHIRGQARFCPHKRLNNAFMLHAST 387
                + N P +F TQS HK  A  SQ S +H ++  +        H R N  FM+H ST
Sbjct: 375 RNGAKDSNGPTVFATQSTHKLLAALSQASMVHVRNGRVP-----IEHSRFNEGFMMHTST 429

Query: 388 SPFYPLFAALDVNAKIHEGESGRRLWAECVEIGIEARKAILARCK------------LFR 435
           SP Y + A+LDV+AK+ +G SG+ L  EC+E  I  R+  +AR               F 
Sbjct: 430 SPLYTIIASLDVSAKMMDGPSGKILTDECIEEAIRFRRT-MARINREIGHRETPSDWWFG 488

Query: 436 PFIPPVV----DGK--LWQDYPTSVLASDRRFFSFEPGAKWHGFEGYAADQYFVDPCKLL 489
            + P  V     GK   + D P  +L  +   +   PG  WHGFEG   D   +DP K+ 
Sbjct: 489 MWQPDAVTDPKSGKRISFTDAPLEILRDNPSCWVLHPGENWHGFEGLEDDYCMLDPIKVT 548

Query: 490 LTTPGIDAETGEYSDFGVPATILAHYLRENGIVPEKCDLNSILFLLTPAESHEKLAQLVA 549
           + TPG+ A+ G    FG+PA ++  +L   GI+ EK    SILFL +   +  K   L+ 
Sbjct: 549 ILTPGV-ADDGRLEPFGIPAALVVKFLDTRGIINEKSGDYSILFLFSVGITKGKWGTLIT 607

Query: 550 MLAQFEQHIEDDSPLVEVLPSVYNKYPVRYRDYTLRQLCQEMHDLYVSFDVKDLQKAMFR 609
            L +F++  ++++ L E+ P +   YP RY   TL +L +EMH      D + L+     
Sbjct: 608 ELFEFKRLYDENTLLEEIFPDLIESYPDRYSGMTLPELAEEMHAF--KRDHRMLETLSQA 665

Query: 610 QQSFPSVVMNPQDAHSAYIRGDVELVRIRDAEGRIAAEGALPYPPGVLCVVPGEVWG--- 666
               P  V+   DA+   +RG VE V +    GR+ A G +PYPPG+  ++PGE  G   
Sbjct: 666 FSLLPEPVITFADAYKRLVRGTVEQVPVEKMGGRVVATGVVPYPPGIPLLLPGERAGDQN 725

Query: 667 GAVQRYFLALEEGVNLLPGFSPELQGV 693
           G +  Y   L++  +  PGF+ +  GV
Sbjct: 726 GPILEYLKGLQDFDSRFPGFNHDTHGV 752


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: 1314
Number of extensions: 66
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: 711
Length of database: 767
Length adjustment: 40
Effective length of query: 671
Effective length of database: 727
Effective search space:   487817
Effective search space used:   487817
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 Sep 24 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