Alignments for a candidate for adiA in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Magnetospirillum magneticum AMB-1

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate WP_011383521.1 AMB_RS05630 amino acid decarboxylase

Query= BRENDA::E8X9U7
         (756 letters)



>NCBI__GCF_000009985.1:WP_011383521.1
          Length = 783

 Score =  436 bits (1120), Expect = e-126
 Identities = 241/748 (32%), Positives = 404/748 (54%), Gaps = 24/748 (3%)

Query: 15  DTWVGNAVERLADALSQQNVTVIKSTSFDDGYAILSANEAIDCLMFSYQMEQPDEHLSVR 74
           D   G  V+++   + +    V+++   +D    +  + AI C++  +  E+  +     
Sbjct: 19  DDLEGVRVQQIITEVERLGFEVVRARRIEDAEIAVQTDAAIGCVLVDW--EKGGKGAEAT 76

Query: 75  QLIGKLHERQQNVPVFLLGDREKATASLDRDLLELVDEFAWILEDTADFIAGRAVAAMTR 134
           +LI  +  R   +P+ +L   E+    +  D+L+ +D + ++ E+T +FIA   V+ + +
Sbjct: 77  ELINLMRRRGLEMPIVILVRGERFE-DIPVDVLDYIDGYVFLAEETPEFIAKNLVSRLKQ 135

Query: 135 YRQQLLPPLFNALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFYHDYYGENLFRSDMGIE 194
           + + L  P F AL+ Y++     W  PGH GG+ + ++P GR + ++ GE +FR D+   
Sbjct: 136 FAETLKTPFFGALVDYAEEGNQLWTCPGHNGGIFYNRSPIGRIFVEHLGEAVFRDDLDNS 195

Query: 195 RTTLGSLLDHTGAFGESEKNAARVFGADRSWSVVVGTSGSNRTIMQACMTDNDVVVLDRN 254
              LG LL H G   +++K AA++FGA++++ V+ GTS SN+ ++ A + ++D+V+ DRN
Sbjct: 196 VLELGDLLTHEGPALQAQKEAAKIFGAEKTYFVLNGTSASNKIVLSALVAEDDLVLFDRN 255

Query: 255 CHKSIEQG-LILTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKISASPLTK-TKAGQ 312
            HK+   G L+L G  P+++   RN  G+IGPIY +    + ++ KI  +PL K  +A +
Sbjct: 256 NHKAAHHGALLLGGGIPIFLETDRNAMGMIGPIYAEAFDEQAIRAKIRDNPLVKDPEAWK 315

Query: 313 KP---SYSVVTNCTYDGVCYNAKEAQDLLAKTSDRIHFDEAWYGYARFNPIYCDHYAM-R 368
           KP     +V+  CTYDG  Y+A+   + +    D I FDEAW G+ +F+P++   Y M  
Sbjct: 316 KPRPFRVAVIEQCTYDGTIYSAEHILERIGHLCDYILFDEAWAGFLKFHPLFRGCYGMGL 375

Query: 369 GEPGDHNGPTVFATHSTHKLLNALSQASYIHVREGR-----GAVNFSRFNQAYMMHATTS 423
            +  D + P + +T STHK +   SQAS IHVR+         +   RFN+ +++HA+TS
Sbjct: 376 KDRLDEDSPGIISTQSTHKQMAGFSQASQIHVRDRHIKGQSRRIEHRRFNETFLLHASTS 435

Query: 424 PLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTDE-----GDWFFK 478
           P Y + AS DV   MM G SG  L  + ID  ++ R+ +  + +EF ++       WFF+
Sbjct: 436 PFYPLFASLDVGAQMMRGRSGEVLWDDTIDLGIELRKKVRAIKREFVEKEKDSARHWFFE 495

Query: 479 PWNKDVVTDPQTGKT-YDFADAPAKLLATDQNCWVMRPGETWHGFKDLP-DNWSMLDPIK 536
           P+  D V  P+ G+T   + D P + +A D   W   PG  WHGFK +    ++M DP K
Sbjct: 496 PFVPDRVPSPEGGETMVAWEDLPTETIAADPRYWEFTPGARWHGFKHVSRSGYAMTDPNK 555

Query: 537 VSILAPGMG-DDGELEASGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTL 595
           ++++ PG   D G     G+PA +V  +L  + +VP +     ++FL + GV   K GTL
Sbjct: 556 LTLITPGFNRDTGAYAEYGIPAPVVAQYLRENRVVPEKNDLNSMLFLLTPGVESSKAGTL 615

Query: 596 INTLCSFKHHYDANTPLAQVMPELVQDYPDTYANMGIHDLGDKMFAWLRENNPGARLNAA 655
           +++L +FK  +D N  L   +PE V+  P  Y  + I DL  +M A+ R+ N      A 
Sbjct: 616 LSSLVAFKRRHDDNALLDDAIPEFVRRRPQRYRGLRIQDLCAEMHAFFRDRNVSTLQRAQ 675

Query: 656 YST--LPVAEITPRDAYNAIVNNNIEMVAIENLPGRIAANSVIPYPPGIPMLLSGENFGD 713
           +S    P   + P DA   +  N ++ + I+ + GRIA    + YPPGI  ++ GE   +
Sbjct: 676 FSPEHRPHMVMRPNDAVRMLTRNQVDYLPIDQIDGRIATTLWVVYPPGIATIIPGERLCE 735

Query: 714 ENSPQVGYLRSLQSWDHHFPGFEHETEG 741
              P + YL+  +   + FPGFE E +G
Sbjct: 736 RARPMLDYLKMFERSANLFPGFEAEIQG 763


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: 1410
Number of extensions: 71
Number of successful extensions: 10
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: 783
Length adjustment: 41
Effective length of query: 715
Effective length of database: 742
Effective search space:   530530
Effective search space used:   530530
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