Alignments for a candidate for cadA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for cadA in Acidovorax sp. GW101-3H11

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate Ac3H11_2914 Arginine decarboxylase (EC 4.1.1.19); Ornithine decarboxylase (EC 4.1.1.17); Lysine decarboxylase (EC 4.1.1.18)

Query= SwissProt::Q9I2S7
         (751 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2914
          Length = 761

 Score =  685 bits (1768), Expect = 0.0
 Identities = 350/761 (45%), Positives = 488/761 (64%), Gaps = 24/761 (3%)

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

Query: 66  AEG----AGEN-QRLLQDVVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQLRG 120
            +      GE    ++  +   I   R +   +PI+  GE  T  + P + + +LH   G
Sbjct: 64  IDDEEFTVGEGLDPIVLSLRNFIGEVRRKNADVPIYVHGETKTSRHLPNDILRELH---G 120

Query: 121 ILYLFEDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKS 180
            +++FEDT  F+AR + R A++YL  + PPFF+AL+++    +YSWH PGH GGVA+ KS
Sbjct: 121 FIHMFEDTPEFVARHIIREAKSYLESVQPPFFKALLDYAEDGSYSWHCPGHSGGVAFLKS 180

Query: 181 PVGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVINGTS 240
           PVGQ +HQF+GEN LR+D+  +V ELG LLDH G + E+E  AAR F ADH FFV NGTS
Sbjct: 181 PVGQMYHQFYGENMLRADVCNAVEELGQLLDHNGAIGESERNAARIFNADHCFFVTNGTS 240

Query: 241 TANKIVWHSMVGREDLVLVDRNCHKSILHSIIMTGAIPLYLTPERNELGIIGPIPLSEFS 300
           T+NK+VWH  V   D+V+VDRNCHKSILHSIIMTGAIP+++ P RN  GIIGPIP SEF 
Sbjct: 241 TSNKMVWHHTVAPGDVVVVDRNCHKSILHSIIMTGAIPVFMKPTRNHFGIIGPIPQSEFE 300

Query: 301 KQSIAAKIAASPLARG---REPKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEA 357
             +I AKI A+PL +G   ++ K ++  +T STYDG+ YN E IK  L   V+ LHFDEA
Sbjct: 301 PAAIQAKIKANPLLKGVDAKKVKPRVLTLTQSTYDGVLYNTETIKGMLDGYVDNLHFDEA 360

Query: 358 WYAYAAFHEFYDGRYGMGTSRSE-EGPLVFATHSTHKMLAAFSQASMIHVQDGGTRKLDV 416
           W  +AAFH FY   + MG  R+  +  + +AT S HK+LA  SQAS + VQD  T KLD 
Sbjct: 361 WLPHAAFHPFYGSYHAMGKKRTRPKYSVTYATQSIHKLLAGISQASHVLVQDSQTAKLDR 420

Query: 417 ARFNEAFMMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVRQNL 476
             FNEA++MH STSPQY IIAS DVA+AMME P G +L++E+  EAL FRRA+  V ++ 
Sbjct: 421 HLFNEAYLMHTSTSPQYSIIASCDVAAAMMEPPGGTALVEESLLEALDFRRAMRQVEEDF 480

Query: 477 DRNDWWFGVWQPEQVEGTDQVGTHDWVL-------EPSADWHGFGDIAEDYVLLDPIKVT 529
            +NDWWF VW P+++         DW++       +  + WHGFG +A+ + +LDPIK T
Sbjct: 481 GKNDWWFKVWGPDKLVDEGLGRAEDWIIRSDGKGKKNGSKWHGFGQLADGFNMLDPIKST 540

Query: 530 LTTPGLSAGGKLSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLVTE 589
           + TPGL+  GK  + GIPA+IV+++L E G+VVEKTGLYSF ++F++GITKG+W+TL+T 
Sbjct: 541 IVTPGLNLDGKFDKTGIPASIVTKYLAEHGVVVEKTGLYSFFIMFTIGITKGRWNTLLTA 600

Query: 590 LLEFKRCYDANLPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKRMYTV 649
           L +FK  Y+ N P+  +LP   Q   KRY  +GLRDL   +H  Y     A+    MY  
Sbjct: 601 LQQFKDDYEKNQPMWRILPEFCQQ-HKRYERMGLRDLCQHVHEMYAKYDIARLTTEMYLS 659

Query: 650 LPEVAMRPSEAYDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGERFTEATRSI 709
               AM+PS+AY  +     E V I  LEGRI   ++ PYPPGIPL++PGE F    + I
Sbjct: 660 DLTPAMKPSDAYAHIAHRTTERVEIDNLEGRITVGLVTPYPPGIPLLIPGEVF---NKKI 716

Query: 710 LDYLEFARTFERAFPGFDSDVHGLQHQDGPSGRC-YTVECI 749
           +DYL+FAR F +  PGF++D+HGL   +  SG+  Y  +C+
Sbjct: 717 VDYLKFAREFAKLCPGFETDIHGLVEVEDESGQVRYYADCV 757


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: 1435
Number of extensions: 48
Number of successful extensions: 9
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: 761
Length adjustment: 40
Effective length of query: 711
Effective length of database: 721
Effective search space:   512631
Effective search space used:   512631
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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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