GapMind for catabolism of small carbon sources

 

Alignments for a candidate for odc in Burkholderia phytofirmans PsJN

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate BPHYT_RS04980 BPHYT_RS04980 lysine decarboxylase

Query= BRENDA::Q5ZH57
         (745 letters)



>FitnessBrowser__BFirm:BPHYT_RS04980
          Length = 761

 Score =  406 bits (1043), Expect = e-117
 Identities = 246/702 (35%), Positives = 366/702 (52%), Gaps = 36/702 (5%)

Query: 39  NRTVVDADNSDFVDVAAVVVMDDEKAIINKADETKFNIPIFII--TDDSSKVDGETMSKI 96
           +  VV+ +  +    AA+V +   +A + +      +IPIF+   T  S  +  + + ++
Sbjct: 74  DNVVVEGETPELA--AAIVAL---RAFVTEVRRRNADIPIFLYGETRTSRHLPNDILREL 128

Query: 97  FHIIDWHNNYDRRLYDREIEAAAKKYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYF 156
              I    +       R I    K Y D + PPFFK L  Y + G+  + CPGH GG  F
Sbjct: 129 HGFIHMFEDTPE-FVARHIIRETKVYLDSLAPPFFKELVQYADEGSYSWHCPGHSGGVAF 187

Query: 157 RKSPAGREFYNFYGENIFRSDICNADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMN 216
            KSP G+ F+ F+GEN+ R+D+CNA  +LG LL H GP   +E++AAR+F+AD  +FV N
Sbjct: 188 LKSPLGQMFHQFFGENMLRADVCNAVDELGQLLDHTGPVAASERNAARIFSADHVFFVTN 247

Query: 217 GTTTSNNIAITAAVAPGDLVLFDRNNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYS 276
           GT+TSN I     VAPGD+VL DRN HKS+ + A+   G  PV+L  +R+++G IG I  
Sbjct: 248 GTSTSNKIVWHGTVAPGDIVLVDRNCHKSILH-AITMTGAIPVFLTPTRNNFGIIGPIPR 306

Query: 277 KDFDEKSIREKI-AKVDPEKAKAKRPF---RLAVIQLGTYDGTIYNAKQVVERIGHLCDY 332
            +F+ ++I++KI A     +A AK P    R+  I   TYDG IYN + + E +G   D 
Sbjct: 307 SEFEPENIKKKILANPFAREALAKNPNLKPRILTITQSTYDGVIYNVEMIKEMLGDWLDT 366

Query: 333 ILFDSAWVGYEQFIPMMKDSSPLLLNLGPDDPGILVTQSTHKQQAGFSQASQIHKKDSHI 392
           + FD AW+ + +F    +D   +          +  T STHK  AG SQASQI  +DS  
Sbjct: 367 LHFDEAWLPHAEFHEFYQDMHAIGAGRPRIGAMVFATHSTHKLLAGISQASQIVVQDSK- 425

Query: 393 KGQKRYINHKQFNNAYMKFSSTSPFYPLFATLDINAKMQEGEAGKKLWHDALVTSVNARK 452
               R+  H+ FN AY+  +STSP Y + A+ D+ A M E   G  L  +++  +++ R+
Sbjct: 426 --NSRFDKHR-FNEAYLMHTSTSPQYAIIASCDVAAAMMEAPGGPALVEESIAEALDFRR 482

Query: 453 NLLKNATMIKPFLPPVVHGKPW------QDADTEKIVSDIDYWKFEKGAKWHGFDGYADN 506
            ++K             +G  W       D   E+ +   + W      +WHGF   ADN
Sbjct: 483 AMIK---------VDAEYGDDWFFKVWGPDQFAEEGIGSREDWMLRPNDEWHGFGPLADN 533

Query: 507 QYFVDPNKFMLTTPGIDVETGEYEDFGIPAVILANYLREHGIIPEKNDLNSILFLMTPAE 566
              +DP K  + TPG+D+  G + + GIPA I+  YL EHGII EK  L S   + T   
Sbjct: 534 FNMLDPIKATIVTPGLDM-GGGFGETGIPAAIVTKYLAEHGIIVEKTGLYSFFIMFTIGI 592

Query: 567 TQAKMDNLVTQIVKFESLVKADAPLDEVLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNN 626
           T+ + +++VT++ +F+     + PL  VLP   S H   YE   ++ LCQ++H  Y+ N+
Sbjct: 593 TKGRWNSMVTELQQFKDDYDNNQPLWRVLPEFVS-HHPMYERVGLRDLCQQIHSVYRAND 651

Query: 627 TKEYQKEMFLGKYFPEQAMTPYQANVELLKNNAKLVPLTDIEGLAALEGALPYPPGIFCI 686
                 EM+L     E AM P  A  +L       VP+ ++EG        PYPPGI  +
Sbjct: 652 IARLTTEMYLSSM--EPAMKPSDAFAKLAHREIDRVPIDELEGRVTSILLTPYPPGIPLL 709

Query: 687 VPGEKWTKVAQKYFLILEESINRFPGFAPEIQGVYFEKENGK 728
           +PGE++ K    Y     E   RFPGF  +I G+  E  NG+
Sbjct: 710 IPGERFNKTIVNYLRFAREFNERFPGFHTDIHGLVGETINGR 751


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: 1292
Number of extensions: 71
Number of successful extensions: 8
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: 761
Length adjustment: 40
Effective length of query: 705
Effective length of database: 721
Effective search space:   508305
Effective search space used:   508305
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