Alignments for a candidate for adiA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Herbaspirillum seropedicae SmR1

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate HSERO_RS17280 HSERO_RS17280 lysine decarboxylase

Query= BRENDA::E8X9U7
         (756 letters)



>FitnessBrowser__HerbieS:HSERO_RS17280
          Length = 750

 Score =  505 bits (1301), Expect = e-147
 Identities = 273/766 (35%), Positives = 428/766 (55%), Gaps = 37/766 (4%)

Query: 4   VLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGYAILSANEAIDCLMFSYQ 63
           ++I++ +F  ++T  G  +  LADA+  + + V+  TS+ D              + S  
Sbjct: 7   IVIIDEDFRSENT-SGLGIRALADAIEAEGMEVLGVTSYGDLAQFAQQQSRASAFILSID 65

Query: 64  MEQ----PDEHL-----SVRQLIGKLHERQQNVPVFLLGDREKATASLDRDLLELVDEFA 114
            E+     DE       ++R  + ++  +  ++P++L G+  + +  +  D+L  +  F 
Sbjct: 66  DEEMGAGSDEETDHALKALRAFVSEIRHKNADIPIYLYGET-RTSRHIPNDVLRELHGFI 124

Query: 115 WILEDTADFIAGRAVAAMTRYRQQLLPPLFNALMKYSDIHEYSWAAPGHQGGVGFTKTPA 174
            + EDT +F+A   +     Y   L PP F AL+ Y+    YSW  PGH GGV F K+P 
Sbjct: 125 HMFEDTPEFVARHIIREAKSYLDGLAPPFFRALVDYAQDGSYSWHCPGHSGGVAFLKSPV 184

Query: 175 GRFYHDYYGENLFRSDMGIERTTLGSLLDHTGAFGESEKNAARVFGADRSWSVVVGTSGS 234
           G+ +H ++GE + R+D+      LG LLDHTG    SE+NAAR+F AD  + V  GTS S
Sbjct: 185 GQMFHQFFGERMLRADVCNAVEELGQLLDHTGPVANSERNAARIFNADHCYFVTNGTSTS 244

Query: 235 NRTIMQACMTDNDVVVLDRNCHKSIEQGLILTGAKPVYMVPSRNRYGIIGPIYPQEMQPE 294
           N+ +  + +   D+VV+DRNCHKSI   +I+TGA PV+++P+RN  GIIGPI  +E   E
Sbjct: 245 NKMVWHSTVAPGDIVVVDRNCHKSILHSIIMTGAIPVFLMPTRNHLGIIGPIPLEEFTLE 304

Query: 295 TLQKKISASPLTKTKAGQKPSYSVVTNCTYDGVCYNAKEAQDLLAKTSDRIHFDEAWYGY 354
           ++QKKI A+P  +    +KP    +T  TYDGV YN +  +D+L    + +HFDEAW  +
Sbjct: 305 SIQKKIEANPFAREAKNKKPRILTITQSTYDGVVYNVETLKDMLDGEIETLHFDEAWLPH 364

Query: 355 ARFNPIYCDHYAMRGEPGDHNGPTVFATHSTHKLLNALSQASYIHVREGRGA-VNFSRFN 413
           A F+  Y D +A+  +        +F+T STHKLL  LSQAS I VRE     ++   FN
Sbjct: 365 ATFHDFYKDMHAIGKDRPRAKKSLIFSTQSTHKLLAGLSQASQILVRESETVKLDEDAFN 424

Query: 414 QAYMMHATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTDEG 473
           +A++MH +TSP Y+I AS DVA +MM+   G +L +E I EA+DFR+AM ++ +EF DE 
Sbjct: 425 EAFLMHTSTSPQYSIIASCDVAAAMMEAPGGTALVEESILEALDFRRAMKKIDQEFGDE- 483

Query: 474 DWFFKPWNKDVVTDPQTGKTYDFADAPAKLLATDQNCWVMRPGETWHGFKDLPDNWSMLD 533
            W+F+ W  +       G+  D               WV++  + WHGF +L   ++MLD
Sbjct: 484 -WWFQVWGPNSFAADGIGERED---------------WVIKAEDDWHGFGNLAPGFNMLD 527

Query: 534 PIKVSILAPGMGDDGELEASGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWG 593
           PIK +I+ PG+  +G+   +G+PA++VT +L  HG++  +   +    +F++G+T+G+W 
Sbjct: 528 PIKATIVNPGLALNGQFGETGIPASIVTKYLAEHGVIVEKCGLYSFFIMFTIGITKGRWN 587

Query: 594 TLINTLCSFKHHYDANTPLAQVMPELVQDYPDTYANMGIHDLGDKMFAWLRENNPGARLN 653
           TL+  L  FK  YD N P+ +++PE  Q  P  Y  +G+ DL  ++    R  +      
Sbjct: 588 TLVTALQQFKDDYDKNQPIWRILPEFAQRNP-RYERLGLRDLCQQIHETYRAYDVARLTT 646

Query: 654 AAYSTLPVAEITPRDAYNAIVNNNIEMVAIENLPGRIAANSVIPYPPGIPMLLSGENFGD 713
             Y +     + P DA++ + +  IE V ++ L GR+ +  + PYPPGIP+L+ GE F  
Sbjct: 647 EMYLSDMQPAMKPSDAFSKMAHREIERVPLDELEGRVTSILLTPYPPGIPLLIPGEIF-- 704

Query: 714 ENSPQVGYLRSLQSWDHHFPGFEHETEG--TEIIDG--VYHVMCVK 755
            N   V YL+  + ++  FPGFE +  G     ++G   Y V CVK
Sbjct: 705 -NKTIVDYLKFARDFNEKFPGFETDVHGLVKREVNGRRDYFVDCVK 749


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: 1434
Number of extensions: 65
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: 756
Length of database: 750
Length adjustment: 40
Effective length of query: 716
Effective length of database: 710
Effective search space:   508360
Effective search space used:   508360
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