Alignments for a candidate for cadA in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for cadA in Methylobacterium nodulans ORS 2060

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate WP_015927042.1 MNOD_RS01410 Orn/Lys/Arg decarboxylase N-terminal domain-containing protein

Query= SwissProt::Q9I2S7
         (751 letters)



>NCBI__GCF_000022085.1:WP_015927042.1
          Length = 786

 Score =  500 bits (1288), Expect = e-145
 Identities = 286/771 (37%), Positives = 422/771 (54%), Gaps = 41/771 (5%)

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

Query: 66  AEGAGENQRLLQDVVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQLRGILYLF 125
               G + +       LI + R R  ++PI  +  +  +E+ P E    L  + G ++L 
Sbjct: 66  WGKRGLDGK----AAALIDMMRQRGLEMPIVIMVRRKRLEDIPVEL---LDFIDGYIFLA 118

Query: 126 EDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKSPVGQA 185
           E+T  F+AR +      Y   L  PFF ALV++  + N  W  PGH GG+ Y +SP+G+ 
Sbjct: 119 EETPEFIARGLVSRVTQYAETLKTPFFGALVDYAEKGNQLWTCPGHNGGIFYNRSPIGRI 178

Query: 186 FHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVINGTSTANKI 245
           F +  GE   R DL  SV +LG LL H GP  +A+  AA  FGA+ T+FV+NGTS +NKI
Sbjct: 179 FVEHLGEAIFRDDLDNSVLDLGDLLTHEGPALKAQKEAAAIFGAEKTYFVLNGTSASNKI 238

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

Query: 305 AAKIAASPLARGREP-----KVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEAWY 359
             KI  +PL R R+        ++AV+   TYDG  Y+A  I   +G   + + FDEAW 
Sbjct: 299 RDKIRRNPLVRDRQAWRRQRPFRVAVIEQCTYDGTIYDAREILARIGHLCDYILFDEAWA 358

Query: 360 AYAAFHEFYDGRYGMG-TSRSEEGPLVFATHSTHKMLAAFSQASMIHVQD----GGTRKL 414
            +  FH  Y GR+ MG      + P + AT STHK LA+FSQAS IH +D    G +R++
Sbjct: 359 GFMKFHPLYAGRFAMGLDGLGPDSPGIIATQSTHKQLASFSQASQIHTKDGHIRGQSRRV 418

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

Query: 475 NLDRND------WWFGVWQPEQVEG------------TDQVGTHD--WVLEPSADWHGFG 514
             + N+      W+F  + P+ VEG            TD + +    W L P A WHGF 
Sbjct: 479 EFEENEADPQRRWFFDPFVPDLVEGPDGTVLPWESLPTDLLASEPRYWELAPGARWHGFT 538

Query: 515 DIAEDYVLLDPIKVTLTTPGLS-AGGKLSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVL 573
            +A  Y + DP K+T+ TPG     G+ +E G+PA IV+++L E  +V EK  L S L L
Sbjct: 539 KVAPGYAITDPNKLTVLTPGFDRETGEYAEHGVPAPIVAQYLRENRIVPEKNDLNSLLFL 598

Query: 574 FSMGITKGKWSTLVTELLEFKRCYDANLPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHAS 633
            + G+   K  TL++ L+ FKR +D N+PL + +P   +   +RY GV LRDL    HA 
Sbjct: 599 LTPGVESSKAGTLISGLVAFKRLHDDNVPLEEAMPDFVRRRPRRYQGVRLRDLCAEFHAF 658

Query: 634 YRDNATAKAMKRMYTV--LPEVAMRPSEAYDKLVRGEVEAVPIARLEGRIAAVMLVPYPP 691
           +R+  T+   ++ +    LPE+AM P  A   L R +V+ VPIA   GRIA  +++ YPP
Sbjct: 659 HREAGTSTLQRKQFAPEHLPEMAMPPKAAAQMLTRNQVDFVPIAEAAGRIATTLMLVYPP 718

Query: 692 GIPLIMPGERFTEATRSILDYLEFARTFERAFPGFDSDVHGLQHQDGPSGR 742
           GI  ++PGER  E  + +LDY     T    FPGF++++ G+  Q  P GR
Sbjct: 719 GIGTVLPGERLDERAKPMLDYFTMFETSANLFPGFEAEIQGVYRQVEPDGR 769


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: 1440
Number of extensions: 71
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: 786
Length adjustment: 41
Effective length of query: 710
Effective length of database: 745
Effective search space:   528950
Effective search space used:   528950
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 Apr 09 2024. 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 2024 update 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