Alignments for a candidate for cadA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for cadA in Herbaspirillum seropedicae SmR1

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate HSERO_RS17280 HSERO_RS17280 lysine decarboxylase

Query= SwissProt::Q9I2S7
         (751 letters)



>FitnessBrowser__HerbieS:HSERO_RS17280
          Length = 750

 Score =  729 bits (1882), Expect = 0.0
 Identities = 364/755 (48%), Positives = 498/755 (65%), Gaps = 17/755 (2%)

Query: 6   KFPVLIVHRDIKADTVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLACILVA 65
           +FP++I+  D +++  +G  +R +A  +E +G  +L   S  +    A      +  +++
Sbjct: 4   RFPIVIIDEDFRSENTSGLGIRALADAIEAEGMEVLGVTSYGDLAQFAQQQSRASAFILS 63

Query: 66  AE----GAG---ENQRLLQDVVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQL 118
            +    GAG   E    L+ +   +   R +   +PI+  GE  T  + P + + +LH  
Sbjct: 64  IDDEEMGAGSDEETDHALKALRAFVSEIRHKNADIPIYLYGETRTSRHIPNDVLRELH-- 121

Query: 119 RGILYLFEDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYR 178
            G +++FEDT  F+AR + R A++YL GL PPFFRALV++    +YSWH PGH GGVA+ 
Sbjct: 122 -GFIHMFEDTPEFVARHIIREAKSYLDGLAPPFFRALVDYAQDGSYSWHCPGHSGGVAFL 180

Query: 179 KSPVGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVING 238
           KSPVGQ FHQFFGE  LR+D+  +V ELG LLDHTGP+A +E  AAR F ADH +FV NG
Sbjct: 181 KSPVGQMFHQFFGERMLRADVCNAVEELGQLLDHTGPVANSERNAARIFNADHCYFVTNG 240

Query: 239 TSTANKIVWHSMVGREDLVLVDRNCHKSILHSIIMTGAIPLYLTPERNELGIIGPIPLSE 298
           TST+NK+VWHS V   D+V+VDRNCHKSILHSIIMTGAIP++L P RN LGIIGPIPL E
Sbjct: 241 TSTSNKMVWHSTVAPGDIVVVDRNCHKSILHSIIMTGAIPVFLMPTRNHLGIIGPIPLEE 300

Query: 299 FSKQSIAAKIAASPLAR-GREPKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEA 357
           F+ +SI  KI A+P AR  +  K ++  +T STYDG+ YN E +K  L   +E LHFDEA
Sbjct: 301 FTLESIQKKIEANPFAREAKNKKPRILTITQSTYDGVVYNVETLKDMLDGEIETLHFDEA 360

Query: 358 WYAYAAFHEFYDGRYGMGTSRSE-EGPLVFATHSTHKMLAAFSQASMIHVQDGGTRKLDV 416
           W  +A FH+FY   + +G  R   +  L+F+T STHK+LA  SQAS I V++  T KLD 
Sbjct: 361 WLPHATFHDFYKDMHAIGKDRPRAKKSLIFSTQSTHKLLAGLSQASQILVRESETVKLDE 420

Query: 417 ARFNEAFMMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVRQNL 476
             FNEAF+MH STSPQY IIAS DVA+AMME P G +L++E+  EAL FRRA+  + Q  
Sbjct: 421 DAFNEAFLMHTSTSPQYSIIASCDVAAAMMEAPGGTALVEESILEALDFRRAMKKIDQEF 480

Query: 477 DRNDWWFGVWQPEQVEGTDQVGTHDWVLEPSADWHGFGDIAEDYVLLDPIKVTLTTPGLS 536
             ++WWF VW P            DWV++   DWHGFG++A  + +LDPIK T+  PGL+
Sbjct: 481 G-DEWWFQVWGPNSFAADGIGEREDWVIKAEDDWHGFGNLAPGFNMLDPIKATIVNPGLA 539

Query: 537 AGGKLSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLVTELLEFKRC 596
             G+  E GIPA+IV+++L E G++VEK GLYSF ++F++GITKG+W+TLVT L +FK  
Sbjct: 540 LNGQFGETGIPASIVTKYLAEHGVIVEKCGLYSFFIMFTIGITKGRWNTLVTALQQFKDD 599

Query: 597 YDANLPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKRMYTVLPEVAMR 656
           YD N P+  +LP  AQ    RY  +GLRDL   +H +YR    A+    MY    + AM+
Sbjct: 600 YDKNQPIWRILPEFAQR-NPRYERLGLRDLCQQIHETYRAYDVARLTTEMYLSDMQPAMK 658

Query: 657 PSEAYDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGERFTEATRSILDYLEFA 716
           PS+A+ K+   E+E VP+  LEGR+ +++L PYPPGIPL++PGE F    ++I+DYL+FA
Sbjct: 659 PSDAFSKMAHREIERVPLDELEGRVTSILLTPYPPGIPLLIPGEIF---NKTIVDYLKFA 715

Query: 717 RTFERAFPGFDSDVHGLQHQDGPSGRCYTVECIKE 751
           R F   FPGF++DVHGL  ++    R Y V+C+K+
Sbjct: 716 RDFNEKFPGFETDVHGLVKREVNGRRDYFVDCVKQ 750


Lambda     K      H
   0.320    0.136    0.407 

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: 1437
Number of extensions: 41
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: 751
Length of database: 750
Length adjustment: 40
Effective length of query: 711
Effective length of database: 710
Effective search space:   504810
Effective search space used:   504810
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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Steps (tab-delimited)
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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