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 SMa0680 SMa0680 amino acid (ornithine, lysine, arginine) decarboxylase

Query= BRENDA::E8X9U7
         (756 letters)



>FitnessBrowser__Smeli:SMa0680
          Length = 782

 Score =  410 bits (1054), Expect = e-118
 Identities = 230/663 (34%), Positives = 363/663 (54%), Gaps = 25/663 (3%)

Query: 110 VDEFAWILEDTADFIAGRAVAAMTRYRQQLLPPLFNALMKYSDIHEYSWAAPGHQGGVGF 169
           VD F ++ + T  F A + ++++  Y + LLPP F  LM Y      ++  PGHQGG  +
Sbjct: 109 VDGFVYLGQQTPAFYAKQIISSLVNYGKTLLPPFFGGLMAYDGEANIAFDCPGHQGGQFY 168

Query: 170 TKTPAGRFYHDYYGENLFRSDMGIERTTLGSLLDHTGAFGESEKNAARVFGADRSWSVVV 229
            K+PAG+ + +Y+GE++FR+D+      LG LL H G   E++KNAAR+FGADR++ ++ 
Sbjct: 169 RKSPAGQLFFNYFGESIFRADLCNADVDLGDLLIHEGPAAEAQKNAARIFGADRTYFILN 228

Query: 230 GTSGSNRTIMQACMTDNDVVVLDRNCHKSIEQG-LILTGAKPVYMVPSRNRYGIIGPIYP 288
           GTS SN+ +  A +   D+V+ DRN HKS+ QG L+  GA PVY+  SRN +G+IG +  
Sbjct: 229 GTSTSNKVVTNAVLRAGDLVLFDRNNHKSLHQGALVQAGAIPVYLPTSRNSFGMIGAVDW 288

Query: 289 QEMQPETLQKKISASPLTKTKA---GQKP-SYSVVTNCTYDGVCYNAKEAQDLLAKTSDR 344
                 +L+++I   PL + KA    ++P   + +   TYDG  YN ++  + +    D 
Sbjct: 289 DAWDEASLRRQIERHPLVEDKARASAERPFRLACIQLATYDGTIYNVRKVLEQIGHLCDY 348

Query: 345 IHFDEAWYGYARFNPIYCDHYAMRGEPGDHNGPTVFATHSTHKLLNALSQASYI-----H 399
           + +DEAW GY  F+P++ DH  MR +  D   P +F+T S HK     SQAS I     H
Sbjct: 349 VLWDEAWIGYNAFHPLFEDHSPMRIDTLDAEMPGLFSTQSVHKQGAGFSQASQIHKRDEH 408

Query: 400 VREGRGAVNFSRFNQAYMMHATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFR 459
           +R+ R  V   RFN++ +MH +TSP Y + AS DV   + +G +G  L    I+  ++ R
Sbjct: 409 IRDQRRYVEHKRFNESLLMHVSTSPFYPLFASLDVNAKIHEGKAGEMLWDRCIELGIEAR 468

Query: 460 QAMARLYKEFTDEG-----DWFFKPWNKDVVTDPQTGKTYDFADA-----PAKLLATDQN 509
           + +    + +   G      WFF P+  DVVT   +  T D  ++     P +++  +Q 
Sbjct: 469 KKLREFTRYYESSGAGPQEQWFFDPFVPDVVTISGSKHTEDVVESRWEALPTEVIKREQQ 528

Query: 510 CWVMRPGETWHGFKDLPDNWSMLDPIKVSILAPGMG-DDGELEASGVPAALVTAWLGRHG 568
           CW  RPG +WHG+    D ++M+DP K+++L PG+    GE    G+PA +V  +L    
Sbjct: 529 CWRFRPGASWHGYSGYSDGYAMVDPNKLTLLTPGIDRATGEYRDFGIPATMVANYLREQR 588

Query: 569 IVPTRTTDFQIMFLFSMGVTRGKWGTLINTLCSFKHHYDANTPLAQVMPELVQDYPDTYA 628
           IVP +     I+FL +      K  TLI  L  FK+ +D + PLA+V+P +     + YA
Sbjct: 589 IVPEKCDLNSILFLLTPAEDESKLNTLIAKLVKFKNLWDRDAPLAEVLPTVFAANRERYA 648

Query: 629 NMGIHDLGDKMFAWLRENNPG--ARLNAAYSTLPVAEITPRDAYNAIVNNNIEMVAIENL 686
              +  +  +M  + R+       RL     ++P   +TP+ AY A+V N ++ VA++  
Sbjct: 649 GYTLRQVCAEMHDFYRQAGVKELQRLCFRAESMPEPAMTPKAAYEALVANEVDYVALDEA 708

Query: 687 PGRIAANSVIPYPPGIPMLLSGENFGDENSPQVGYLRSLQSWDHHFPGFEHETEGT--EI 744
            GRI+A   + YPPGI +++ GE + +   P   Y  + Q   + FPGF +E +G   E 
Sbjct: 709 FGRISATLALIYPPGIGVIVPGERWDERARPMHNYFLAFQESFNRFPGFNYEVQGVFQER 768

Query: 745 IDG 747
           +DG
Sbjct: 769 VDG 771


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: 1454
Number of extensions: 79
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: 756
Length of database: 782
Length adjustment: 41
Effective length of query: 715
Effective length of database: 741
Effective search space:   529815
Effective search space used:   529815
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