GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS04980 BPHYT_RS04980 lysine
           decarboxylase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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