GapMind for catabolism of small carbon sources

 

Alignments for a candidate for odc in Dechlorosoma suillum PS

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate Dsui_1245 Dsui_1245 arginine/lysine/ornithine decarboxylase

Query= BRENDA::Q5ZH57
         (745 letters)



>FitnessBrowser__PS:Dsui_1245
          Length = 746

 Score =  402 bits (1034), Expect = e-116
 Identities = 238/683 (34%), Positives = 370/683 (54%), Gaps = 30/683 (4%)

Query: 63  KAIINKADETKFNIPIFII--TDDSSKVDGETMSKIFHIIDWHNNYDRRLYDREIEAAAK 120
           +A +++       IPIF+   T  S  +  + + ++   I  + +    +  R +   AK
Sbjct: 83  RAFVSEIRLRNSEIPIFLHGETRTSRHIPNDVLRELHGFIHMYEDTPEFIA-RNVVREAK 141

Query: 121 KYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGENIFRSDICN 180
            Y + + PPFF+AL  Y   G+  + CPGH GG  F KSP G+ F+ F+GEN+ R+D+CN
Sbjct: 142 AYLESLPPPFFRALTHYASDGSYSWHCPGHSGGVAFLKSPVGQMFHQFFGENMLRADVCN 201

Query: 181 ADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAPGDLVLFDR 240
           A  +LG LL H GP   +E++AAR+FN D  YFV NGT+TSN I   + VAPGD+V+ DR
Sbjct: 202 AVEELGQLLDHTGPVAASERNAARIFNCDHLYFVTNGTSTSNKIVWHSTVAPGDIVVVDR 261

Query: 241 NNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKIAKVDPEKAKAKR 300
           N HKS+ + A++  G  PV+L  +R+++G IG I   +F  ++I++KIA       K  +
Sbjct: 262 NCHKSILH-AIMMTGAIPVFLMPTRNNFGIIGPIPKSEFAWENIQKKIAANPFATDKNAK 320

Query: 301 PFRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPMMKDSSPLLLNLG 360
           P R+  I   TYDG +YN + + E +    D + FD AW+ +  F     D       +G
Sbjct: 321 P-RVLTITQSTYDGILYNVEAIKEELDGKIDTLHFDEAWLPHAAFHDFYGDYHA----IG 375

Query: 361 PDDPG-----ILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNAYMKFSSTS 415
            D P      +  TQSTHK  AG SQASQI  +D+    +  +++   FN AY+  +STS
Sbjct: 376 ADRPRCKESMVFSTQSTHKLLAGLSQASQILVQDA----ENSHLDRDVFNEAYLMHTSTS 431

Query: 416 PFYPLFATLDINAKMQEGEAGKKLWHDALVTSVNARKNLLKNATMIKPFLPPVVHGKPWQ 475
           P Y + A+ D+ A M E   G  L  +++  +++ R+ + K    +          K W 
Sbjct: 432 PQYAIIASCDVAAAMMEEPGGTALVEESIAEALDFRRAMRK----VDEEWGSGWWFKVWG 487

Query: 476 DAD-TEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGIDVETGEYEDFGI 534
             D +E+ + + D W  + G +WHGF   AD    +DP K  + TPG+DV+ GE+ + GI
Sbjct: 488 PDDLSEEGIEERDAWMLKPGDRWHGFGNLADGFNMLDPIKATIITPGLDVD-GEFAERGI 546

Query: 535 PAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKFESLVKADAPLDEV 594
           PA I+  YL EHG+I EK  L S   + T   T+ + +++VT++ +F+     + PL +V
Sbjct: 547 PAAIVTKYLAEHGVIVEKCGLYSFFIMFTIGITKGRWNSMVTELQQFKDDYDKNQPLWKV 606

Query: 595 LPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFPEQAMTPYQANVEL 654
           LP   ++H  RYE   ++ LC+E+H  Y++N+      EM+L    P  AM P  A  ++
Sbjct: 607 LPAFVAKH-PRYERVGLRDLCREIHAVYRSNDVARLTTEMYLSDMVP--AMKPADAFAKM 663

Query: 655 LKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKWTKVAQKYFLILEESINRFPGFA 714
                  VP+ ++EG        PYPPGI  ++PGE++ +   +Y     +   +FPGF 
Sbjct: 664 AHREIDRVPIDELEGRVTSVLLTPYPPGIPLLIPGERFNRTIMQYLQFARDFNEKFPGFE 723

Query: 715 PEIQGVYFEKENGKSVAYGYVYD 737
            +I G+  E+ +GK    GY  D
Sbjct: 724 TDIHGLVKEERDGK---VGYYVD 743


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: 52
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: 746
Length adjustment: 40
Effective length of query: 705
Effective length of database: 706
Effective search space:   497730
Effective search space used:   497730
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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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