Alignments for a candidate for adiA in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Methylobacterium nodulans ORS 2060

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate WP_015927042.1 MNOD_RS01410 Orn/Lys/Arg decarboxylase N-terminal domain-containing protein

Query= BRENDA::P28629
         (755 letters)



>NCBI__GCF_000022085.1:WP_015927042.1
          Length = 786

 Score =  442 bits (1138), Expect = e-128
 Identities = 249/745 (33%), Positives = 403/745 (54%), Gaps = 22/745 (2%)

Query: 14  DTWVGNAVERLADALSQQNVTVIKSTSFDDGFAILSSNEAIDCLMFSYQMEHPDEHQNVR 73
           D   G  V ++  A+  +   V+++   +D    + ++ AI C++  +     D      
Sbjct: 19  DDLEGARVNQIVAAVEARGFEVVRARRVEDAAIAVQTDAAIGCMVVDWGKRGLDG--KAA 76

Query: 74  QLIGKLHERQQNVPVFLLGDREKALAAMDRDLLELVDEFAWILEDTADFIAGRAVAAMTR 133
            LI  + +R   +P+ ++  R K L  +  +LL+ +D + ++ E+T +FIA   V+ +T+
Sbjct: 77  ALIDMMRQRGLEMPIVIMV-RRKRLEDIPVELLDFIDGYIFLAEETPEFIARGLVSRVTQ 135

Query: 134 YRQQLLPPLFSALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFYHDYYGENLFRTDMGIE 193
           Y + L  P F AL+ Y++     W  PGH GG+ + ++P GR + ++ GE +FR D+   
Sbjct: 136 YAETLKTPFFGALVDYAEKGNQLWTCPGHNGGIFYNRSPIGRIFVEHLGEAIFRDDLDNS 195

Query: 194 RTSLGSLLDHTGAFGESEKYAARVFGADRSWSVVVGTSGSNRTIMQACMTDNDVVVVDRN 253
              LG LL H G   +++K AA +FGA++++ V+ GTS SN+ ++ A + ++D+V+ DRN
Sbjct: 196 VLDLGDLLTHEGPALKAQKEAAAIFGAEKTYFVLNGTSASNKIVLSALVAEDDLVLFDRN 255

Query: 254 CHKSIEQG-LMLTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKISESPLTKDKAG-- 310
            HK+   G L L G  P+++   RN +G+IGPIY +      ++ KI  +PL +D+    
Sbjct: 256 NHKAAHHGALFLGGGIPIFLETDRNAHGLIGPIYHEAFDEAAIRDKIRRNPLVRDRQAWR 315

Query: 311 -QKP-SYCVVTNCTYDGVCYNAKEAQDLLEKTSDRLHFDEAWYGYARFNPIYADHYAMRG 368
            Q+P    V+  CTYDG  Y+A+E    +    D + FDEAW G+ +F+P+YA  +AM  
Sbjct: 316 RQRPFRVAVIEQCTYDGTIYDAREILARIGHLCDYILFDEAWAGFMKFHPLYAGRFAMGL 375

Query: 369 EPGDHNGPTVFATHSTHKLLNALSQASYIHVREG--RG---AINFSRFNQAYMMHATTSP 423
           +    + P + AT STHK L + SQAS IH ++G  RG    +   R N+++++HA+TSP
Sbjct: 376 DGLGPDSPGIIATQSTHKQLASFSQASQIHTKDGHIRGQSRRVEHRRLNESFLVHASTSP 435

Query: 424 LYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTADGS-----WFFKP 478
            Y + AS DV   MM G SG+ L  + I   +++R+ +  + KEF  + +     WFF P
Sbjct: 436 FYPLFASLDVGAQMMKGRSGMILWDDTIRLGIEWRKKVRAIRKEFEENEADPQRRWFFDP 495

Query: 479 WNKEVVTDPQTGKTYDFADAPTKLLTTVQDCWVMHPGESWHGFKDIPDNWSMLDPIKVSI 538
           +  ++V  P  G    +   PT LL +    W + PG  WHGF  +   +++ DP K+++
Sbjct: 496 FVPDLVEGPD-GTVLPWESLPTDLLASEPRYWELAPGARWHGFTKVAPGYAITDPNKLTV 554

Query: 539 LAPGMG-EDGELEETGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLVNT 597
           L PG   E GE  E GVPA +V  +L  + IVP +     ++FL + GV   K GTL++ 
Sbjct: 555 LTPGFDRETGEYAEHGVPAPIVAQYLRENRIVPEKNDLNSLLFLLTPGVESSKAGTLISG 614

Query: 598 LCSFKRHYDANTPLAQVMPELVEQYPDTYANMGIHDLGDTMFAWLKENNPGA--RLNEAY 655
           L +FKR +D N PL + MP+ V + P  Y  + + DL     A+ +E       R   A 
Sbjct: 615 LVAFKRLHDDNVPLEEAMPDFVRRRPRRYQGVRLRDLCAEFHAFHREAGTSTLQRKQFAP 674

Query: 656 SGLPVAEVTPREAYNAIVDNNVELVSIENLPGRIAANSVIPYPPGIPMLLSGENFGDKNS 715
             LP   + P+ A   +  N V+ V I    GRIA   ++ YPPGI  +L GE   ++  
Sbjct: 675 EHLPEMAMPPKAAAQMLTRNQVDFVPIAEAAGRIATTLMLVYPPGIGTVLPGERLDERAK 734

Query: 716 PQVSYLRSLQSWDHHFPGFEHETEG 740
           P + Y    ++  + FPGFE E +G
Sbjct: 735 PMLDYFTMFETSANLFPGFEAEIQG 759


Lambda     K      H
   0.319    0.135    0.414 

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: 1456
Number of extensions: 75
Number of successful extensions: 7
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: 755
Length of database: 786
Length adjustment: 41
Effective length of query: 714
Effective length of database: 745
Effective search space:   531930
Effective search space used:   531930
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 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. 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:

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 2024 update 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