Alignments for a candidate for cadA in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for cadA in Azospirillum brasilense Sp245

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate AZOBR_RS27535 AZOBR_RS27535 amino acid decarboxylase

Query= SwissProt::Q9I2S7
         (751 letters)



>FitnessBrowser__azobra:AZOBR_RS27535
          Length = 785

 Score =  511 bits (1316), Expect = e-149
 Identities = 293/775 (37%), Positives = 427/775 (55%), Gaps = 42/775 (5%)

Query: 6   KFPVLIVHRDIKADTVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLACILVA 65
           +F  L+       D + G RV+ I  E+E+ GF ++ T    +  +   T   + C++V 
Sbjct: 6   RFSFLVCAPAFDPDELEGVRVQQIVAEVERLGFEVVRTRRVEDAELAIRTDAAIGCMIVD 65

Query: 66  AEGAGENQRLLQDVVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQLRGILYLF 125
               G    L      LI +AR R  ++PI  L  +  +EN P +    L+Q+ G ++L 
Sbjct: 66  WGKRG----LEGKPASLIALARKRGLEMPIILLVRRQRLENIPVDV---LNQVDGYVFLA 118

Query: 126 EDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKSPVGQA 185
           E+T  F+A+ +    + Y   L  PFF  LV++  + N  W  PGH GG+ Y +SP+G+ 
Sbjct: 119 EETPEFIAKNLVSRLKQYAETLKTPFFGELVDYAEEGNQLWTCPGHNGGIFYSRSPIGRI 178

Query: 186 FHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVINGTSTANKI 245
           F +  GE   R D+  SV E+G LL H GP  +A+  AA+ FGA+ T+FV+NGTS +NKI
Sbjct: 179 FVEHLGEAVFRDDIDNSVLEMGDLLVHEGPALKAQKEAAKIFGAERTYFVLNGTSASNKI 238

Query: 246 VWHSMVGREDLVLVDRNCHKSILH-SIIMTGAIPLYLTPERNELGIIGPIPLSEFSKQSI 304
           V  ++V  +DLVL DRN HK+  H  + + G IP++L  +RN  G+IGPI      ++ I
Sbjct: 239 VLSALVAEDDLVLFDRNNHKAAHHGGLFLGGGIPVFLETDRNAYGLIGPIDHEALDEERI 298

Query: 305 AAKIAASPLARG-----REPKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEAWY 359
            AKI  +PL +      RE   + AV+   +YDG  Y+AE I   +G   + + FDEAW 
Sbjct: 299 RAKIRGNPLVKDPDAWKRERPFRAAVIQQCSYDGTIYSAETILAKIGHLCDYILFDEAWA 358

Query: 360 AYAAFHEFYDGRYGMGTSRSEEG-PLVFATHSTHKMLAAFSQASMIHVQD----GGTRKL 414
            +  FH  + GR+ MG     +G P + AT STHK LA+FSQAS IHV+D    G  R++
Sbjct: 359 GFLKFHPLFKGRFAMGLDGLHDGHPGIIATQSTHKQLASFSQASQIHVKDSHIRGQRRRV 418

Query: 415 DVARFNEAFMMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVRQ 474
           +  RFNE F++H STSP Y + ASLDV + MM+G +G  L  +T    +  R+ +  +R+
Sbjct: 419 EHRRFNETFLLHASTSPFYPLFASLDVGAQMMKGRSGEVLWDDTIRLGVELRKKIRAIRR 478

Query: 475 NLDRND------WWFGVWQPEQVE-----------GTDQVGT--HDWVLEPSADWHGFGD 515
             +  +      W+F  + P++V             TD + +    WV +P A WHGF  
Sbjct: 479 EFEERESAPARRWFFDPFVPDRVSFDGAEIAWEEVPTDALASDVRHWVFKPGAHWHGFRH 538

Query: 516 IAEDYVLLDPIKVTLTTPGLS-AGGKLSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLF 574
           +A  Y + DP K+TL TPG     G   E GIPA +V+++L E  +V EK  L S L L 
Sbjct: 539 VAAGYAMTDPNKLTLLTPGFDRRTGAYEEHGIPAPVVAQYLRENRIVPEKNDLNSILFLL 598

Query: 575 SMGITKGKWSTLVTELLEFKRCYDANLPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASY 634
           + G+   K  TL++ L+ FKR +D N  L DV+P        RY G  LRDL   MH  Y
Sbjct: 599 TPGVESSKAGTLLSALVAFKRLHDDNALLEDVIPEFVARRPARYAGRRLRDLCAEMHGFY 658

Query: 635 RDNATAKAMKRMYTV--LPEVAMRPSEAYDKLVRGEVEAVPIARLEGRIAAVMLVPYPPG 692
           R+  T +  +RM+    LPE+ M P EA  +LVR +V+ +PI R+ GR+A  + V YPPG
Sbjct: 659 RERRTNELQRRMFRPDHLPEMVMPPREAVRRLVRNDVDYLPIDRIAGRVATTLFVVYPPG 718

Query: 693 IPLIMPGERFTEATRSILDYLEFARTFERAFPGFDSDVHGLQHQDGPSG--RCYT 745
           I  I+PGER  E  R +++YL+  +     FPGFD+++ GL  +  P G  R YT
Sbjct: 719 IATIVPGERLDERARPMIEYLQVFQEGANRFPGFDNEIQGLYRETEPDGSVRFYT 773


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: 1397
Number of extensions: 50
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: 751
Length of database: 785
Length adjustment: 41
Effective length of query: 710
Effective length of database: 744
Effective search space:   528240
Effective search space used:   528240
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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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