Alignments for a candidate for odc in Derxia gummosa DSM 723

GapMind for catabolism of small carbon sources

Alignments for a candidate for odc in Derxia gummosa DSM 723

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate WP_028310072.1 H566_RS0101800 lysine decarboxylase

Query= BRENDA::Q5ZH57
         (745 letters)



>NCBI__GCF_000482785.1:WP_028310072.1
          Length = 755

 Score =  385 bits (989), Expect = e-111
 Identities = 249/761 (32%), Positives = 381/761 (50%), Gaps = 51/761 (6%)

Query: 1   MDSEINDDSVHQTNLPHKFSTDELKIASTAHATAYFDT----------NRTVVDADNSDF 50
           +D +   ++V  + +       E +   T   T++ DT          +  ++  D+ +F
Sbjct: 10  IDEDFRSENVSGSGIRALAEAIEAEGVETVGVTSFSDTAMFAQQQSRASGFILSIDDDEF 69

Query: 51  VDVAAVVVMDDEKAIIN------KADETKFNIPIFII--TDDSSKVDGETMSKIFHIIDW 102
               + V  + ++AI+N      +      +IPIF+   T  S  +  + + ++   I  
Sbjct: 70  ---NSDVPQEQQQAIVNLRAFVGEIRHRNADIPIFLYGETRTSRHIPNDVLRELHGFIHM 126

Query: 103 HNNYDRRLYDREIEAAAKKYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAG 162
             +       R I   A+ Y D + PPFF+AL  Y + G+  + CPGH GG  F KSP G
Sbjct: 127 FEDTPE-FVARHIIREARAYLDSLPPPFFRALTHYAQDGSYSWHCPGHSGGVAFLKSPVG 185

Query: 163 REFYNFYGENIFRSDICNADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSN 222
           + F+ F+GEN+ R+D+CNA  +LG LL H GP   +E++AAR+F +D  +FV NGT+TSN
Sbjct: 186 QMFHQFFGENMLRADVCNAVEELGQLLDHTGPVAASERNAARIFGSDHLFFVTNGTSTSN 245

Query: 223 NIAITAAVAPGDLVLFDRNNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEK 282
            I   + VAPGD+V+ DRN HKSV + +++  G  PV+L  +R++ G IG I   +F  +
Sbjct: 246 KIVWHSTVAPGDIVVVDRNCHKSVLH-SIIMIGAIPVFLMPTRNNLGIIGPIPLAEFTPE 304

Query: 283 SIREK-----IAKVDPEKAKAKRPFRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDS 337
           +IR K     IA   PE  KAK   R+  I   TYDG +YN + +   +    D ++FD 
Sbjct: 305 AIRAKIEAHPIASKLPEHVKAKP--RILTITQSTYDGVMYNVEAIKGLLDGRIDTLMFDE 362

Query: 338 AWVGYEQFIPMMKDSSPLLLNLGPDDPG-----ILVTQSTHKQQAGFSQASQIHKKDSHI 392
           AW+ +  F     D       +G D P      +  TQSTHK  AG SQASQI  +DS  
Sbjct: 363 AWLPHAAFHDFYGDFHA----IGKDRPRCKESMLFATQSTHKLLAGLSQASQILVQDSEQ 418

Query: 393 KGQKRYINHKQFNNAYMKFSSTSPFYPLFATLDINAKMQEGEAGKKLWHDALVTSVNARK 452
            G    ++H +FN AY+  +STSP Y + A+ DI A M E   G  L  +++V +++ R+
Sbjct: 419 NG----LDHYRFNEAYLMHTSTSPQYAIIASCDIAAAMMEPPGGPALVEESIVEALDFRR 474

Query: 453 NLLKNATMIKPFLPPVVHGKPWQDAD-TEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVD 511
            + K    +          K W   D ++  + D D W+      WHGF   A     +D
Sbjct: 475 AMRK----VDQEFGADWWFKVWGPDDISDDGMPDPDEWELRGDEHWHGFGKLAPGFNMLD 530

Query: 512 PNKFMLTTPGIDVETGEYEDFGIPAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKM 571
           P K  + TPG+DV+    ++FGIPA I+  YL EHG+I EK  L S   + T   T+ + 
Sbjct: 531 PIKATIVTPGLDVDGNFSDEFGIPAGIVNKYLAEHGVIVEKTGLYSFFIMFTIGITKGRW 590

Query: 572 DNLVTQIVKFESLVKADAPLDEVLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQ 631
           + LVT + +F+     +A L  +LP     H  RYE   ++ LC+++H  Y+  +     
Sbjct: 591 NTLVTALQQFKDDYDKNAQLWRILPEFVQAH-PRYERMGLRDLCEQIHGMYRRFDVARLT 649

Query: 632 KEMFLGKYFPEQAMTPYQANVELLKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEK 691
            EM+  K   E  M P  A   +       VP+ ++EG        PYPPGI  ++PGE+
Sbjct: 650 TEMYTSKM--EPVMKPADAFAAMAHREIDRVPVDELEGRVTSILLTPYPPGIPLLIPGER 707

Query: 692 WTKVAQKYFLILEESINRFPGFAPEIQGVYFEKENGKSVAY 732
           + +    Y     E    FPGF  ++ G+  EK+   S  Y
Sbjct: 708 FNRTIVDYLRFTREFNAAFPGFETDVHGLVAEKQPDGSKKY 748


Lambda     K      H
   0.318    0.136    0.405 

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: 1294
Number of extensions: 56
Number of successful extensions: 7
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: 745
Length of database: 755
Length adjustment: 40
Effective length of query: 705
Effective length of database: 715
Effective search space:   504075
Effective search space used:   504075
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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 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