Alignments for a candidate for odc in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for odc in Sinorhizobium meliloti 1021

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate SMa0682 SMa0682 decarboxylase (lysine, ornithine, arginine)

Query= BRENDA::Q5ZH57
         (745 letters)



>FitnessBrowser__Smeli:SMa0682
          Length = 756

 Score =  366 bits (939), Expect = e-105
 Identities = 231/687 (33%), Positives = 349/687 (50%), Gaps = 45/687 (6%)

Query: 76  IPIFIITDDSSKVDGETMSKIFHIIDWHNNYDRRLYD-------REIEAAAKKYEDGVLP 128
           +PIF+  DD+      T   +   +  H N   RL++       R I  AA+ Y + + P
Sbjct: 93  LPIFLFGDDT------TAEMVPAPVLRHANAFMRLFEDSPEFMARAIVRAAQNYLERLPP 146

Query: 129 PFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGENIFRSDICNADVDLGDL 188
           P FKAL  Y   G   +  PGH GG  FRKSP G+ FY F+GEN  RSDI  +   +G L
Sbjct: 147 PMFKALMEYTLHGAYSWHTPGHGGGVAFRKSPVGQLFYTFFGENTLRSDISVSVGSVGSL 206

Query: 189 LIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAPGDLVLFDRNNHKSVYN 248
           L H GP  + E++AAR+F AD+T FV+ GT+T+N I     V   DLVL DRN HKS+ +
Sbjct: 207 LDHVGPIGEGERNAARIFGADETLFVVGGTSTANKIVWQGMVTRNDLVLCDRNCHKSILH 266

Query: 249 AALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKIAKVDPEKAKAKRPFRLAVIQ 308
            +L+  G  P+YL  SR+  G IG I  + F  ++I  KI    P  ++     RL V+ 
Sbjct: 267 -SLIMTGATPIYLTPSRNGLGIIGPIAKEQFTPEAIAHKIV-ASPFASETNGKVRLMVVT 324

Query: 309 LGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPMMKDSSPLLLNLGP---DDPG 365
             TYDG  YN   +   +G   + + FD AW  Y  F     D    + +  P    +  
Sbjct: 325 NSTYDGLCYNVDGIKSALGDAVEVLHFDEAWFAYANFHEFY-DGYHAISSTKPARSQEAI 383

Query: 366 ILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNAYMKFSSTSPFYPLFATLD 425
              TQSTHK  A FSQAS +H + +  K     ++  +FN A+M  +STSP Y + A+ D
Sbjct: 384 TFATQSTHKLLAAFSQASMLHVQHAVAK----QLDITRFNEAFMMHTSTSPQYGIIASCD 439

Query: 426 INAKMQEGEAGKKLWHDAL------VTSVNARKNLLKNATMIKPFLPPVVHGKPWQDADT 479
           + A M E  AG+ L  + +        +VNA +  ++++   + + PP+    P  DA +
Sbjct: 440 VAAAMMEQPAGRALVQETIDEAMSFRRAVNAVRTQMQDSWWFEVWEPPIADRAP-SDATS 498

Query: 480 EKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGIDVETGEYEDFGIPAVIL 539
           +        W  + G  WHGF+  A+N   VDP K  + +PG++   G   + GIPA ++
Sbjct: 499 D--------WLLKPGDAWHGFEDLAENHVMVDPIKVTILSPGLNA-GGAMLEHGIPAAVV 549

Query: 540 ANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKFESLVKADAPLDEVLPRLY 599
             +L    I  EK  L S L L +   T+ K   L+T+++ F+ L  A+APL   LP L 
Sbjct: 550 TKFLSSRRIEIEKTGLYSFLVLFSMGITRGKWSTLITELLNFKDLYDANAPLSRALPALA 609

Query: 600 SEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFPEQAMTPYQANVELLKNNA 659
           + H D Y    ++ LC+++HD Y+++     Q+EM+     PE A+ P  A   L+K   
Sbjct: 610 AAHPDVYRAMGLRDLCEKIHDVYRSDGVPNAQREMY--TVLPEMALRPADAYNRLVKGCV 667

Query: 660 KLVPLTDIEGLAALEGALPYPPGIFCIVPGEK---WTKVAQKYFLILEESINRFPGFAPE 716
           + V + ++ G       +PYPPGI  I+PGE+    T+  Q Y +       +FPGF  +
Sbjct: 668 ESVDIDELIGRTLAVMIVPYPPGIPLIMPGERITAATRSIQDYLVYARSFDRKFPGFETD 727

Query: 717 IQGVYF-EKENGKSVAYGYVYDKSKDE 742
           I G+ F    +G+      + ++ +D+
Sbjct: 728 IHGLRFVANPSGRRYLVDCIVEEGQDD 754


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: 1198
Number of extensions: 53
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: 745
Length of database: 756
Length adjustment: 40
Effective length of query: 705
Effective length of database: 716
Effective search space:   504780
Effective search space used:   504780
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 17 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