Alignments for a candidate for adiA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Burkholderia phytofirmans PsJN

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate BPHYT_RS04980 BPHYT_RS04980 lysine decarboxylase

Query= BRENDA::E8X9U7
         (756 letters)



>FitnessBrowser__BFirm:BPHYT_RS04980
          Length = 761

 Score =  531 bits (1368), Expect = e-155
 Identities = 289/778 (37%), Positives = 438/778 (56%), Gaps = 50/778 (6%)

Query: 4   VLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGYAILSANEAIDCLMFSY- 62
           V+I++ +F  ++   G+ +  LA+A+ ++   V+  TS+ D  +    +    C + S  
Sbjct: 7   VVIIDEDFRSENI-SGSGIRALAEAIEKEGAEVLGLTSYGDLTSFAQQSSRASCFILSID 65

Query: 63  -------------QMEQPD---EHLSVRQLIGKLHERQQNVPVFLLGDREKATASLDRDL 106
                        + E P+     +++R  + ++  R  ++P+FL G+  + +  L  D+
Sbjct: 66  DDELLPYVDNVVVEGETPELAAAIVALRAFVTEVRRRNADIPIFLYGET-RTSRHLPNDI 124

Query: 107 LELVDEFAWILEDTADFIAGRAVAAMTRYRQQLLPPLFNALMKYSDIHEYSWAAPGHQGG 166
           L  +  F  + EDT +F+A   +     Y   L PP F  L++Y+D   YSW  PGH GG
Sbjct: 125 LRELHGFIHMFEDTPEFVARHIIRETKVYLDSLAPPFFKELVQYADEGSYSWHCPGHSGG 184

Query: 167 VGFTKTPAGRFYHDYYGENLFRSDMGIERTTLGSLLDHTGAFGESEKNAARVFGADRSWS 226
           V F K+P G+ +H ++GEN+ R+D+      LG LLDHTG    SE+NAAR+F AD  + 
Sbjct: 185 VAFLKSPLGQMFHQFFGENMLRADVCNAVDELGQLLDHTGPVAASERNAARIFSADHVFF 244

Query: 227 VVVGTSGSNRTIMQACMTDNDVVVLDRNCHKSIEQGLILTGAKPVYMVPSRNRYGIIGPI 286
           V  GTS SN+ +    +   D+V++DRNCHKSI   + +TGA PV++ P+RN +GIIGPI
Sbjct: 245 VTNGTSTSNKIVWHGTVAPGDIVLVDRNCHKSILHAITMTGAIPVFLTPTRNNFGIIGPI 304

Query: 287 YPQEMQPETLQKKISASPLTKTKAGQ----KPSYSVVTNCTYDGVCYNAKEAQDLLAKTS 342
              E +PE ++KKI A+P  +    +    KP    +T  TYDGV YN +  +++L    
Sbjct: 305 PRSEFEPENIKKKILANPFAREALAKNPNLKPRILTITQSTYDGVIYNVEMIKEMLGDWL 364

Query: 343 DRIHFDEAWYGYARFNPIYCDHYAMRGEPGDHNGPTVFATHSTHKLLNALSQASYIHVRE 402
           D +HFDEAW  +A F+  Y D +A+ G      G  VFATHSTHKLL  +SQAS I V++
Sbjct: 365 DTLHFDEAWLPHAEFHEFYQDMHAI-GAGRPRIGAMVFATHSTHKLLAGISQASQIVVQD 423

Query: 403 GRGA-VNFSRFNQAYMMHATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQA 461
            + +  +  RFN+AY+MH +TSP YAI AS DVA +MM+   G +L +E I EA+DFR+A
Sbjct: 424 SKNSRFDKHRFNEAYLMHTSTSPQYAIIASCDVAAAMMEAPGGPALVEESIAEALDFRRA 483

Query: 462 MARLYKEFTDEGDWFFKPWNKDVVTDPQTGKTYDFADAPAKLLATDQNCWVMRPGETWHG 521
           M ++  E+ D  DWFFK W  D   +   G   D               W++RP + WHG
Sbjct: 484 MIKVDAEYGD--DWFFKVWGPDQFAEEGIGSRED---------------WMLRPNDEWHG 526

Query: 522 FKDLPDNWSMLDPIKVSILAPGMGDDGELEASGVPAALVTAWLGRHGIVPTRTTDFQIMF 581
           F  L DN++MLDPIK +I+ PG+   G    +G+PAA+VT +L  HGI+  +T  +    
Sbjct: 527 FGPLADNFNMLDPIKATIVTPGLDMGGGFGETGIPAAIVTKYLAEHGIIVEKTGLYSFFI 586

Query: 582 LFSMGVTRGKWGTLINTLCSFKHHYDANTPLAQVMPELVQDYPDTYANMGIHDLGDKMFA 641
           +F++G+T+G+W +++  L  FK  YD N PL +V+PE V  +P  Y  +G+ DL  ++ +
Sbjct: 587 MFTIGITKGRWNSMVTELQQFKDDYDNNQPLWRVLPEFVSHHP-MYERVGLRDLCQQIHS 645

Query: 642 WLRENNPGARLNAAYSTLPVAEITPRDAYNAIVNNNIEMVAIENLPGRIAANSVIPYPPG 701
             R N+        Y +     + P DA+  + +  I+ V I+ L GR+ +  + PYPPG
Sbjct: 646 VYRANDIARLTTEMYLSSMEPAMKPSDAFAKLAHREIDRVPIDELEGRVTSILLTPYPPG 705

Query: 702 IPMLLSGENFGDENSPQVGYLRSLQSWDHHFPGFEHETEGT--EIIDG--VYHVMCVK 755
           IP+L+ GE F   N   V YLR  + ++  FPGF  +  G   E I+G   Y V CV+
Sbjct: 706 IPLLIPGERF---NKTIVNYLRFAREFNERFPGFHTDIHGLVGETINGRIEYFVDCVR 760


Lambda     K      H
   0.319    0.135    0.415 

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: 1473
Number of extensions: 72
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: 756
Length of database: 761
Length adjustment: 40
Effective length of query: 716
Effective length of database: 721
Effective search space:   516236
Effective search space used:   516236
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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