Alignments for a candidate for odc in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for odc in Cupriavidus basilensis 4G11

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate RR42_RS15940 RR42_RS15940 lysine decarboxylase

Query= BRENDA::Q5ZH57
         (745 letters)



>FitnessBrowser__Cup4G11:RR42_RS15940
          Length = 754

 Score =  418 bits (1074), Expect = e-121
 Identities = 254/707 (35%), Positives = 378/707 (53%), Gaps = 35/707 (4%)

Query: 42  VVDADNSDFV---DVAAVVVMDDEKAIINKADETKFNIPIFII--TDDSSKVDGETMSKI 96
           +V  D+ +FV   D      ++  +A +N+      ++PIF+   T  S  +  + + ++
Sbjct: 61  IVSIDDDEFVSEDDRPEAAAIEKLRAFVNEVRRRNTDLPIFLYGETRTSRHIPNDILREL 120

Query: 97  FHIIDWHNNYDRRLYDREIEAAAKKYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYF 156
              I    +       R I   A+ Y D + PPFFKAL AY +  +  + CPGH GG  F
Sbjct: 121 HGFIHMFEDTPE-FVARHIIREARVYLDSLAPPFFKALIAYAQDSSYSWHCPGHSGGVAF 179

Query: 157 RKSPAGREFYNFYGENIFRSDICNADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMN 216
            KSP G+ F+ F+GEN+ R+D+CNA  +LG LL H GP   +E++AAR+FN+D  YFV N
Sbjct: 180 LKSPVGQVFHQFFGENMLRADVCNAVDELGQLLDHTGPVAASERNAARIFNSDHMYFVTN 239

Query: 217 GTTTSNNIAITAAVAPGDLVLFDRNNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYS 276
           GT+TSN +   A VAPGD+V+ DRN HKS+ + A++  G  PV+L  +R+ YG IG I  
Sbjct: 240 GTSTSNKMVWHANVAPGDIVVVDRNCHKSILH-AIMMTGAIPVFLMPTRNHYGIIGPIPK 298

Query: 277 KDFDEKSIREKIAKVD-PEKAKAKRPFRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILF 335
            +FD ++IR KIA      +AK ++P R+  I  GTYDG +YNA+Q+ E +    D + F
Sbjct: 299 SEFDPETIRRKIAAHPFASQAKNQKP-RILTITQGTYDGVLYNAEQIKEMLATEIDTLHF 357

Query: 336 DSAWVGYEQFIPMMKDSSPLLLNLGPDDPG-----ILVTQSTHKQQAGFSQASQIHKKDS 390
           D AW+ +  F     D    +  +G D P      +  TQSTHK  AG SQASQI  +DS
Sbjct: 358 DEAWLPHAAF----HDFYHNMHAIGRDRPRSKDALVFATQSTHKLLAGLSQASQILVQDS 413

Query: 391 HIKGQKRYINHKQFNNAYMKFSSTSPFYPLFATLDINAKMQEGEAGKKLWHDALVTSVNA 450
             +   RY    +FN AY+  +STSP Y + A+ D+ A M E   G  L  +++  +++ 
Sbjct: 414 DTRKLDRY----RFNEAYLMHTSTSPQYSIIASCDVAAAMMEAPGGTALVEESIQEAMDF 469

Query: 451 RKNLLKNATMIKPFLPPVVHGKPW-----QDADTEKIVSDIDYWKFEKGAKWHGFDGYAD 505
           R+ + K    ++       +G  W      +A  E  + D + W  +   +WHGF   AD
Sbjct: 470 RRAMRK----VEGDYDAGNNGDWWFKVWGPEALAEDDIGDREEWMLKANERWHGFGDLAD 525

Query: 506 NQYFVDPNKFMLTTPGIDVETGEYEDFGIPAVILANYLREHGIIPEKNDLNSILFLMTPA 565
               +DP K  + TPG+DV+ GE+ D GIPA I+  YL EHGII EK  L S   + T  
Sbjct: 526 GFNLLDPIKATIITPGLDVD-GEFSDRGIPAAIVTKYLAEHGIIIEKTGLYSFFIMFTIG 584

Query: 566 ETQAKMDNLVTQIVKFESLVKADAPLDEVLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNN 625
            T+ + ++LVT++ +F+     + PL  VLP    +H  +YE   ++ LC  +H  YK N
Sbjct: 585 ITKGRWNSLVTELQQFKDDYDQNQPLWRVLPEFVGKH-PQYEKLGLRDLCDAIHSVYKAN 643

Query: 626 NTKEYQKEMFLGKYFPEQAMTPYQANVELLKNNAKLVPLTDIEGLAALEGALPYPPGIFC 685
           +      EM+L     E AM P  A   +     + V + ++EG        PYPPGI  
Sbjct: 644 DVARVTTEMYLSDM--EPAMKPSDAWAMMAHREIERVAVDELEGRVTAILLTPYPPGIPL 701

Query: 686 IVPGEKWTKVAQKYFLILEESINRFPGFAPEIQGVYFEKENGKSVAY 732
           ++PGE++ ++  +Y     E    FPGF  +I G+  E+  G   AY
Sbjct: 702 LIPGERFNRIIVQYLKFAREFNKLFPGFETDIHGLVEEEVEGGGKAY 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: 1314
Number of extensions: 58
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: 754
Length adjustment: 40
Effective length of query: 705
Effective length of database: 714
Effective search space:   503370
Effective search space used:   503370
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