Alignments for a candidate for adiA in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Dechlorosoma suillum PS

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate Dsui_1245 Dsui_1245 arginine/lysine/ornithine decarboxylase

Query= BRENDA::P28629
         (755 letters)



>FitnessBrowser__PS:Dsui_1245
          Length = 746

 Score =  514 bits (1324), Expect = e-150
 Identities = 284/764 (37%), Positives = 430/764 (56%), Gaps = 36/764 (4%)

Query: 3   VLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDD--GFAILSSNEA-----ID 55
           V+I++ +F  ++   G  +  LA+A+  + + V+  TS+ D   FA   S  +     ID
Sbjct: 7   VIIIDEDFRSENA-SGLGIRALAEAIQAEGLEVLGVTSYGDLTSFAQQQSRASTFILSID 65

Query: 56  CLMFSYQMEHPDEHQNVRQLIGKLHERQQNVPVFLLGDREKALAAMDRDLLELVDEFAWI 115
              FS           +R  + ++  R   +P+FL G+   +   +  D+L  +  F  +
Sbjct: 66  DEEFSSPEASAKAIAGLRAFVSEIRLRNSEIPIFLHGETRTS-RHIPNDVLRELHGFIHM 124

Query: 116 LEDTADFIAGRAVAAMTRYRQQLLPPLFSALMKYSDIHEYSWAAPGHQGGVGFTKTPAGR 175
            EDT +FIA   V     Y + L PP F AL  Y+    YSW  PGH GGV F K+P G+
Sbjct: 125 YEDTPEFIARNVVREAKAYLESLPPPFFRALTHYASDGSYSWHCPGHSGGVAFLKSPVGQ 184

Query: 176 FYHDYYGENLFRTDMGIERTSLGSLLDHTGAFGESEKYAARVFGADRSWSVVVGTSGSNR 235
            +H ++GEN+ R D+      LG LLDHTG    SE+ AAR+F  D  + V  GTS SN+
Sbjct: 185 MFHQFFGENMLRADVCNAVEELGQLLDHTGPVAASERNAARIFNCDHLYFVTNGTSTSNK 244

Query: 236 TIMQACMTDNDVVVVDRNCHKSIEQGLMLTGAKPVYMVPSRNRYGIIGPIYPQEMQPETL 295
            +  + +   D+VVVDRNCHKSI   +M+TGA PV+++P+RN +GIIGPI   E   E +
Sbjct: 245 IVWHSTVAPGDIVVVDRNCHKSILHAIMMTGAIPVFLMPTRNNFGIIGPIPKSEFAWENI 304

Query: 296 QKKISESPLTKDKAGQKPSYCVVTNCTYDGVCYNAKEAQDLLEKTSDRLHFDEAWYGYAR 355
           QKKI+ +P   DK   KP    +T  TYDG+ YN +  ++ L+   D LHFDEAW  +A 
Sbjct: 305 QKKIAANPFATDK-NAKPRVLTITQSTYDGILYNVEAIKEELDGKIDTLHFDEAWLPHAA 363

Query: 356 FNPIYADHYAMRGEPGDHNGPTVFATHSTHKLLNALSQASYIHVREGRGA-INFSRFNQA 414
           F+  Y D++A+  +        VF+T STHKLL  LSQAS I V++   + ++   FN+A
Sbjct: 364 FHDFYGDYHAIGADRPRCKESMVFSTQSTHKLLAGLSQASQILVQDAENSHLDRDVFNEA 423

Query: 415 YMMHATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTADGSW 474
           Y+MH +TSP YAI AS DVA +MM+   G +L +E I EA+DFR+AM ++ +E+     W
Sbjct: 424 YLMHTSTSPQYAIIASCDVAAAMMEEPGGTALVEESIAEALDFRRAMRKVDEEW--GSGW 481

Query: 475 FFKPWNKEVVTDPQTGKTYDFADAPTKLLTTVQDCWVMHPGESWHGFKDIPDNWSMLDPI 534
           +FK W  + +++    +               +D W++ PG+ WHGF ++ D ++MLDPI
Sbjct: 482 WFKVWGPDDLSEEGIEE---------------RDAWMLKPGDRWHGFGNLADGFNMLDPI 526

Query: 535 KVSILAPGMGEDGELEETGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTL 594
           K +I+ PG+  DGE  E G+PAA+VT +L  HG++  +   +    +F++G+T+G+W ++
Sbjct: 527 KATIITPGLDVDGEFAERGIPAAIVTKYLAEHGVIVEKCGLYSFFIMFTIGITKGRWNSM 586

Query: 595 VNTLCSFKRHYDANTPLAQVMPELVEQYPDTYANMGIHDLGDTMFAWLKENNPGARLNEA 654
           V  L  FK  YD N PL +V+P  V ++P  Y  +G+ DL   + A  + N+      E 
Sbjct: 587 VTELQQFKDDYDKNQPLWKVLPAFVAKHP-RYERVGLRDLCREIHAVYRSNDVARLTTEM 645

Query: 655 YSGLPVAEVTPREAYNAIVDNNVELVSIENLPGRIAANSVIPYPPGIPMLLSGENFGDKN 714
           Y    V  + P +A+  +    ++ V I+ L GR+ +  + PYPPGIP+L+ GE F   N
Sbjct: 646 YLSDMVPAMKPADAFAKMAHREIDRVPIDELEGRVTSVLLTPYPPGIPLLIPGERF---N 702

Query: 715 SPQVSYLRSLQSWDHHFPGFEHETEG--TEIIDGI--YHVMCVK 754
              + YL+  + ++  FPGFE +  G   E  DG   Y+V CV+
Sbjct: 703 RTIMQYLQFARDFNEKFPGFETDIHGLVKEERDGKVGYYVDCVR 746


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: 1482
Number of extensions: 87
Number of successful extensions: 6
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: 746
Length adjustment: 40
Effective length of query: 715
Effective length of database: 706
Effective search space:   504790
Effective search space used:   504790
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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