GapMind for catabolism of small carbon sources

 

Alignments for a candidate for odc in Amantichitinum ursilacus IGB-41

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate WP_053939388.1 WG78_RS18835 arginine/lysine/ornithine decarboxylase

Query= BRENDA::Q5ZH57
         (745 letters)



>NCBI__GCF_001294205.1:WP_053939388.1
          Length = 756

 Score =  383 bits (984), Expect = e-110
 Identities = 236/672 (35%), Positives = 361/672 (53%), Gaps = 35/672 (5%)

Query: 75  NIPIFII--TDDSSKVDGETMSKIFHIIDWHNNYDRRLYDREIEAAAKKYEDGVLPPFFK 132
           +IPI++   T  +  +  + + ++   I  H +       R I   A+ Y D + PPFF+
Sbjct: 97  DIPIYLYGETRTARHIPNDVLRELHGFIHMHEDTPE-FVARHIIREARSYLDTLAPPFFR 155

Query: 133 ALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGENIFRSDICNADVDLGDLLIHE 192
           AL  Y + G+  + CPGH GG  F KSP G+ F+ F+GEN+ R+D+CNA  +LG LL H 
Sbjct: 156 ALTHYAQDGSYSWHCPGHSGGVAFLKSPVGQMFHQFFGENMLRADVCNAVDELGQLLDHT 215

Query: 193 GPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAPGDLVLFDRNNHKSVYNAALV 252
           GP   +E++AAR+FNAD  +FV NGT+TSN I   + VAPGD+V+ DRN HKS+ + A++
Sbjct: 216 GPVAASERNAARIFNADHLFFVTNGTSTSNKIVWNSTVAPGDIVVVDRNCHKSILH-AIM 274

Query: 253 QAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKIAKVDP---EKAKAK---RPFRLAV 306
             G  PV+L  +R+ YG IG I   +F+ ++IR K+   +P   EK +A    +P R+  
Sbjct: 275 MTGAVPVFLMPTRNHYGIIGPIPRSEFEPENIRRKML-ANPFCREKLEADPDVKP-RVLT 332

Query: 307 IQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPMMKDSSPLLLNLGPDDPG- 365
           I   TYDG +YN +++   +    + + FD AW+ +  F     D       +G   P  
Sbjct: 333 ITQSTYDGIMYNVEEIKGLLDGKIETLHFDEAWLPHAAFHDFYGDYHA----IGEGRPRC 388

Query: 366 ----ILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNAYMKFSSTSPFYPLF 421
               I  TQSTHK  AG SQASQI  +D+    Q+  ++   FN AY+  +STSP Y + 
Sbjct: 389 KESMIFSTQSTHKLLAGLSQASQILVQDA----QENQLDRDIFNEAYLMHTSTSPQYAII 444

Query: 422 ATLDINAKMQEGEAGKKLWHDALVTSVNARKNLLKNATMIKPFLPPVVHGKPWQDAD-TE 480
           A+ D+ A M E   G  L  ++L  +++ R+ + K    +          K W  AD T+
Sbjct: 445 ASCDVAAAMMEAPGGTALVEESLSEALDFRRAMRK----VDEEYGDSWWFKVWGPADLTD 500

Query: 481 KIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGIDVETGEYEDFGIPAVILA 540
           + +   D W  + G +WHGF   A+    +DP K  + TPG+++  G++ + GIPA I++
Sbjct: 501 EGLDHRDAWMLKAGEEWHGFGDVAEGFNMLDPIKATIITPGLNM-AGDFAETGIPASIVS 559

Query: 541 NYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKFESLVKADAPLDEVLPRLYS 600
            YL EHG++ EK  L S   L T   T+ + + L+T + +F+     +APL  +LP  + 
Sbjct: 560 KYLAEHGVVIEKTGLYSFFILFTIGITKGRWNTLLTALQQFKDDYDKNAPLWRILPE-FV 618

Query: 601 EHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFPEQAMTPYQANVELLKNNAK 660
           +   +YE   ++ LCQ++H  YK  +      EM+L    P  A+ P +A  ++     +
Sbjct: 619 QQFPQYERIGLRDLCQQIHGIYKARDVARLTTEMYLSDLVP--ALKPAKAFAKMAHREIE 676

Query: 661 LVPLTDIEGLAALEGALPYPPGIFCIVPGEKWTKVAQKYFLILEESINRFPGFAPEIQGV 720
            VPL ++EG        PYPPGI  ++PGE +     +Y     E  N FPGF   I G+
Sbjct: 677 RVPLDELEGRITAVMLTPYPPGIPLLIPGEVFNHTIVQYLKFAREFNNNFPGFETYIHGL 736

Query: 721 YFEKENGKSVAY 732
              KE G + AY
Sbjct: 737 VAVKE-GNTTAY 747


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: 1291
Number of extensions: 54
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
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 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