Alignments for a candidate for adiA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Sinorhizobium meliloti 1021

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate SMa0682 SMa0682 decarboxylase (lysine, ornithine, arginine)

Query= BRENDA::E8X9U7
         (756 letters)



>FitnessBrowser__Smeli:SMa0682
          Length = 756

 Score =  545 bits (1404), Expect = e-159
 Identities = 288/731 (39%), Positives = 417/731 (57%), Gaps = 23/731 (3%)

Query: 19  GNAVERLADALSQQNVTVIKSTSFDDGYAILSANEAIDCLMFSYQMEQPDEHL--SVRQL 76
           G  +  LA+A+ ++   V+   +++D   +++      C + S    +        + +L
Sbjct: 23  GRGMRSLAEAIEKEGYRVVAGLTYEDARRLVNVFNTESCWLISVDGTESSTTRWEILAEL 82

Query: 77  IGKLHERQQNVPVFLLGDREKATASLDRDLLELVDEFAWILEDTADFIAGRAVAAMTRYR 136
           +     R   +P+FL GD +     +   +L   + F  + ED+ +F+A   V A   Y 
Sbjct: 83  LAAKRSRNNLLPIFLFGD-DTTAEMVPAPVLRHANAFMRLFEDSPEFMARAIVRAAQNYL 141

Query: 137 QQLLPPLFNALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFYHDYYGENLFRSDMGIERT 196
           ++L PP+F ALM+Y+    YSW  PGH GGV F K+P G+ ++ ++GEN  RSD+ +   
Sbjct: 142 ERLPPPMFKALMEYTLHGAYSWHTPGHGGGVAFRKSPVGQLFYTFFGENTLRSDISVSVG 201

Query: 197 TLGSLLDHTGAFGESEKNAARVFGADRSWSVVVGTSGSNRTIMQACMTDNDVVVLDRNCH 256
           ++GSLLDH G  GE E+NAAR+FGAD +  VV GTS +N+ + Q  +T ND+V+ DRNCH
Sbjct: 202 SVGSLLDHVGPIGEGERNAARIFGADETLFVVGGTSTANKIVWQGMVTRNDLVLCDRNCH 261

Query: 257 KSIEQGLILTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKISASPLTKTKAGQKPSY 316
           KSI   LI+TGA P+Y+ PSRN  GIIGPI  ++  PE +  KI ASP      G K   
Sbjct: 262 KSILHSLIMTGATPIYLTPSRNGLGIIGPIAKEQFTPEAIAHKIVASPFASETNG-KVRL 320

Query: 317 SVVTNCTYDGVCYNAKEAQDLLAKTSDRIHFDEAWYGYARFNPIYCDHYAMRG-EPGDHN 375
            VVTN TYDG+CYN    +  L    + +HFDEAW+ YA F+  Y  ++A+   +P    
Sbjct: 321 MVVTNSTYDGLCYNVDGIKSALGDAVEVLHFDEAWFAYANFHEFYDGYHAISSTKPARSQ 380

Query: 376 GPTVFATHSTHKLLNALSQASYIHVREG-RGAVNFSRFNQAYMMHATTSPLYAICASNDV 434
               FAT STHKLL A SQAS +HV+      ++ +RFN+A+MMH +TSP Y I AS DV
Sbjct: 381 EAITFATQSTHKLLAAFSQASMLHVQHAVAKQLDITRFNEAFMMHTSTSPQYGIIASCDV 440

Query: 435 AVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTDEGDWFFKPWNKDVVTDPQTGKTY 494
           A +MM+  +G +L QE IDEA+ FR+A+  +  +  D   W+F+ W   +     +  T 
Sbjct: 441 AAAMMEQPAGRALVQETIDEAMSFRRAVNAVRTQMQD--SWWFEVWEPPIADRAPSDATS 498

Query: 495 DFADAPAKLLATDQNCWVMRPGETWHGFKDLPDNWSMLDPIKVSILAPGMGDDGELEASG 554
           D               W+++PG+ WHGF+DL +N  M+DPIKV+IL+PG+   G +   G
Sbjct: 499 D---------------WLLKPGDAWHGFEDLAENHVMVDPIKVTILSPGLNAGGAMLEHG 543

Query: 555 VPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLINTLCSFKHHYDANTPLAQ 614
           +PAA+VT +L    I   +T  +  + LFSMG+TRGKW TLI  L +FK  YDAN PL++
Sbjct: 544 IPAAVVTKFLSSRRIEIEKTGLYSFLVLFSMGITRGKWSTLITELLNFKDLYDANAPLSR 603

Query: 615 VMPELVQDYPDTYANMGIHDLGDKMFAWLRENNPGARLNAAYSTLPVAEITPRDAYNAIV 674
            +P L   +PD Y  MG+ DL +K+    R +         Y+ LP   + P DAYN +V
Sbjct: 604 ALPALAAAHPDVYRAMGLRDLCEKIHDVYRSDGVPNAQREMYTVLPEMALRPADAYNRLV 663

Query: 675 NNNIEMVAIENLPGRIAANSVIPYPPGIPMLLSGENFGDENSPQVGYLRSLQSWDHHFPG 734
              +E V I+ L GR  A  ++PYPPGIP+++ GE           YL   +S+D  FPG
Sbjct: 664 KGCVESVDIDELIGRTLAVMIVPYPPGIPLIMPGERITAATRSIQDYLVYARSFDRKFPG 723

Query: 735 FEHETEGTEII 745
           FE +  G   +
Sbjct: 724 FETDIHGLRFV 734


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: 1414
Number of extensions: 57
Number of successful extensions: 5
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: 756
Length adjustment: 40
Effective length of query: 716
Effective length of database: 716
Effective search space:   512656
Effective search space used:   512656
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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Steps (tab-delimited)
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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