Alignments for a candidate for cadA in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for cadA in Magnetospirillum magneticum AMB-1

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate WP_011383521.1 AMB_RS05630 amino acid decarboxylase

Query= SwissProt::Q9I2S7
         (751 letters)



>NCBI__GCF_000009985.1:WP_011383521.1
          Length = 783

 Score =  498 bits (1282), Expect = e-145
 Identities = 285/767 (37%), Positives = 424/767 (55%), Gaps = 47/767 (6%)

Query: 19  DTVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLACILVAAEGAGENQRLLQD 78
           D + G RV+ I  E+E+ GF ++      +  I   T   + C+LV  E  G+      +
Sbjct: 19  DDLEGVRVQQIITEVERLGFEVVRARRIEDAEIAVQTDAAIGCVLVDWEKGGKGA----E 74

Query: 79  VVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQLRGILYLFEDTVPFLARQVAR 138
             ELI + R R  ++PI  L      E+ P +    L  + G ++L E+T  F+A+ +  
Sbjct: 75  ATELINLMRRRGLEMPIVILVRGERFEDIPVDV---LDYIDGYVFLAEETPEFIAKNLVS 131

Query: 139 AARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKSPVGQAFHQFFGENTLRSD 198
             + +   L  PFF ALV++  + N  W  PGH GG+ Y +SP+G+ F +  GE   R D
Sbjct: 132 RLKQFAETLKTPFFGALVDYAEEGNQLWTCPGHNGGIFYNRSPIGRIFVEHLGEAVFRDD 191

Query: 199 LSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVINGTSTANKIVWHSMVGREDLVL 258
           L  SV ELG LL H GP  +A+  AA+ FGA+ T+FV+NGTS +NKIV  ++V  +DLVL
Sbjct: 192 LDNSVLELGDLLTHEGPALQAQKEAAKIFGAEKTYFVLNGTSASNKIVLSALVAEDDLVL 251

Query: 259 VDRNCHKSILH-SIIMTGAIPLYLTPERNELGIIGPIPLSEFSKQSIAAKIAASPLARGR 317
            DRN HK+  H ++++ G IP++L  +RN +G+IGPI    F +Q+I AKI  +PL +  
Sbjct: 252 FDRNNHKAAHHGALLLGGGIPIFLETDRNAMGMIGPIYAEAFDEQAIRAKIRDNPLVKDP 311

Query: 318 EP-----KVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEAWYAYAAFHEFYDGRY 372
           E        ++AV+   TYDG  Y+AE I + +G   + + FDEAW  +  FH  + G Y
Sbjct: 312 EAWKKPRPFRVAVIEQCTYDGTIYSAEHILERIGHLCDYILFDEAWAGFLKFHPLFRGCY 371

Query: 373 GMGTS--RSEEGPLVFATHSTHKMLAAFSQASMIHVQD----GGTRKLDVARFNEAFMMH 426
           GMG      E+ P + +T STHK +A FSQAS IHV+D    G +R+++  RFNE F++H
Sbjct: 372 GMGLKDRLDEDSPGIISTQSTHKQMAGFSQASQIHVRDRHIKGQSRRIEHRRFNETFLLH 431

Query: 427 ISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVRQNLDRND------ 480
            STSP Y + ASLDV + MM G +G  L  +T D  +  R+ +  +++     +      
Sbjct: 432 ASTSPFYPLFASLDVGAQMMRGRSGEVLWDDTIDLGIELRKKVRAIKREFVEKEKDSARH 491

Query: 481 WWFGVWQPEQVE----GTDQVGTHD------------WVLEPSADWHGFGDIAED-YVLL 523
           W+F  + P++V     G   V   D            W   P A WHGF  ++   Y + 
Sbjct: 492 WFFEPFVPDRVPSPEGGETMVAWEDLPTETIAADPRYWEFTPGARWHGFKHVSRSGYAMT 551

Query: 524 DPIKVTLTTPGLSAG-GKLSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGK 582
           DP K+TL TPG +   G  +E GIPA +V+++L E  +V EK  L S L L + G+   K
Sbjct: 552 DPNKLTLITPGFNRDTGAYAEYGIPAPVVAQYLRENRVVPEKNDLNSMLFLLTPGVESSK 611

Query: 583 WSTLVTELLEFKRCYDANLPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKA 642
             TL++ L+ FKR +D N  L D +P   +   +RY G+ ++DL   MHA +RD   +  
Sbjct: 612 AGTLLSSLVAFKRRHDDNALLDDAIPEFVRRRPQRYRGLRIQDLCAEMHAFFRDRNVSTL 671

Query: 643 MKRMYTV--LPEVAMRPSEAYDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGE 700
            +  ++    P + MRP++A   L R +V+ +PI +++GRIA  + V YPPGI  I+PGE
Sbjct: 672 QRAQFSPEHRPHMVMRPNDAVRMLTRNQVDYLPIDQIDGRIATTLWVVYPPGIATIIPGE 731

Query: 701 RFTEATRSILDYLEFARTFERAFPGFDSDVHGLQHQDGPSG--RCYT 745
           R  E  R +LDYL+        FPGF++++ GL  +  P G  R YT
Sbjct: 732 RLCERARPMLDYLKMFERSANLFPGFEAEIQGLYREIEPDGSIRFYT 778


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: 1375
Number of extensions: 57
Number of successful extensions: 12
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: 783
Length adjustment: 41
Effective length of query: 710
Effective length of database: 742
Effective search space:   526820
Effective search space used:   526820
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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